FASTA Sequence Format
How to cite this record FAIRsharing.org: FASTA; FASTA Sequence Format; DOI: https://doi.org/10.25504/FAIRsharing.rz4vfg; Last edited: Jan. 8, 2019, 1:34 p.m.; Last accessed: Jul 24 2021 12:04 a.m.
Record updated: Nov. 21, 2018, 9:52 a.m. by The FAIRsharing Team.
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GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. GenBank is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
Animal Transcription Factor Database
AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transcription factors and chromatin remodelling factors.
Apo and Holo structures DataBase
AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo structures; while structures determined in the unbound state are named apo structures.
Aspergillus Genome Database
The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fungal research community.
Bitter Compounds Database
BitterDB is a free and searchable database of bitter compounds. Compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste re- ceptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness.
Bacterial protein tYrosine Kinase database
The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation.
Central Aspergillus Data REpository
This project aims to support the international Aspergillus research community by gathering all genomic information regarding this significant genus into one resource - The Central Aspergillus REsource (CADRE). CADRE facilitates visualisation and analyses of data using the Ensembl software suite. Much of our data has been extracted from Genbank and augmented with the consent of the original sequencing groups. This additional work has been carried out using both automated and manual efforts, with support from specific annotation projects and the general Aspergillus community.
CAPS-DB : a structural classification of helix-capping motifs
CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.
CoryneRegNet 6.0 - Corynebacterial Regulation Network
Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.
Dragon Antimicrobial Peptide Database
Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.
DataBase of Transcriptional Start Sites
This database includes TSS data from adult and embryonic human tissue. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures.
DNA Data Bank of Japan
An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
Human Disease-Related Viral Integration Sites
Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromesome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to cooresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps.
EcoliWiki: A Wiki-based community resource for Escherichia coli
EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
Eukaryotic Linear Motifs
This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs), are compact protein interaction sites composed of short stretches of adjacent amino acids.
Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs.
DRSC Functional Genomics Resources
DRSC Functional Genomics Resources (DRSC-FGR) began as the Drosophila RNAi Screening Center (DRSC), founded by Prof. Norbert Perrimon in 2003, and the Transgenic RNAi Project (TRiP), founded by Prof. Perrimon in 2008. DRSC-FGR has been previously known as flyRNAi.org. It has since grown into a functional genomics platform meeting the needs of the Drosophila and broader community.
Fungal and Oomycete genomics resource
FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.
FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies
A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.
T-DNA insertions in Arabidopsis and their flanking sequence tags.
GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.
Human Gene and Protein Database
Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.
Human Histone Database
HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.
Integrative and Conjugative Elements in Bacteria
A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database called ICEberg. This database contains detailed information on all archived ICEs and the genes carried by each entity, including unique identifiers, species details and hyperlink-paths to other public databases, like NCBI, UniprotKB and KEGG.
Intrinsically Disordered proteins with Extensive Annotations and Literature
IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and post-translational modification sites together with references and structural domain assignments.
Integrated Microbial Genomes And Microbiomes
The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a set of publicly available genome and metagenome datasets. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M.
InterEvol database : Diving into the structure and evolution of protein complex interfaces
Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of tools and resources.
The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes.
This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFBSs). For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.
Minimotif Miner 3.0
A database of short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.
Molecular INTeraction database
MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT is an ELIXIR Core Resource.
Major Intrinsic Proteins Modification Database
This is a database of comparative protein structure models of the MIP (Major Intrinsic Protein) family of proteins. The MIPs have been identified from the completed genome sequence of organisms available at NCBI.
mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.
MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data mining queries spanning many different sources. It is primarily concerned with data for mammals, zebrafish and yeasts.
modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.
A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publically available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt,that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians.
NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationships; human exosome lncRNA expression profiles; and predicted RNA secondary structures of human transcripts. This resource has not been updated since 2017, and therefore its status has been marked as Uncertain. Please get in touch if you have any information about the current status of this resource.
Families of nuclear hormone receptors
Online GEne Essentiality database
Online GEne Essentiality database
GENI-ACT is a resource that allows the research community to collaboratively annotate bacterial genomes. Changes can be suggested to existing genomes and these alterations can be ported back to NCBI Genbank. GENI-ACT also has modules which can be used for educational purposes.
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.
Prokaryotic Glycoproteins Database
ProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized eubacterial and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner.
Protein-Chemical Structural Interactions
Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.
This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.
Saccharomyces Genome Database
The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.
Simple Modular Architecture Research Tool
SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.
SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification.
Search Tool for Interactions of Chemicals
STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
Group II introns database
Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides information on their boundaries, host genes, and secondary structures. In addition, the website provides tools for analysis that may be useful to researchers who encounter group II introns in DNA sequences.
Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.
BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.
Compilation and Creation of datasets from PDB
ccPDB (Compilation and Creation of datasets from PDB) is a collection of commonly used data sets for structural or functional annotation of proteins. There are numerous datasets from the literature and the Protein Data Bank (PDB), which were used for developing methods to annotate proteins at the sequence (or residue) level. A tool is available for creating a wide range of customized data sets from PDB.
Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orthologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera).
Death Domain Database
Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.
GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.
miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other databases and publications.
MitoZoa is a specialized database collecting complete and nearly-complete (longer than 7 kb) mtDNA entries of metazoan species, excluding Placozoa. MitoZoa contains curated entries, whose gene annotation has been significantly improved using a semi-automatic reannotation pipeline and by manual curation of mitogenomics experts. MitoZoa has been specifically designed to address comparative analyses of mitochondrial genomic features in a given metazoan group or in species belonging to the same genus (congeneric species). MitoZoa focuses on mitochondrial gene order, non-coding regions, gene content, and gene sequences.
Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum Nematoda". While Nematode.net started as a project site, over the years it became a community resource dedicated to the study of parasitic nematodes.
SitEx database of eukaryotic protein functional sites
SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.
The SpliceDisease database provides information linking RNA splicing to human disease, including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases.
VIRsiRNAdb contains information on experimentally validated Viral siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.
Ebola and Hemorrhagic Fever Virus Database
The Ebola and Hemorrhagic Fever Virus Database stems from the Hemorrhagic Fever Viruses (HFV) Database Project founded by Dr. Carla Kuiken in 2009 at the Los Alamos National Laboratory (LANL). The HFV Database was modeled on the Los Alamos HIV Database, led by Dr. Bette Korber, and translated much of its tools, infrastructure and philosophy from HIV to HFV.
PASS2 contains alignments of structural motifs of protein superfamilies. PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies). PASS2 contains alignments of protein structures at the superfamily level and is in direct correspondence with SCOPe 2.04 release.
PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.
Prokaryotic Operon DataBase
The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 prokaryotic genomes.
TTD, Therapeutic Target Database
The Therapeutic Target Database provides information about therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information is fully referenced.
The UCSC Archaeal Genome Browser
The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.
Virulence Factor Database
VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).
Virus Pathogen Database and Analysis Resource
The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.
The Yeast Metabolome DataBase
The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.
A comprehensive online knowledgebase for the monkey research community.
IPD-IMGT/HLA - Human Leukocyte Antigen Sequence Database
The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database was established to provide a locus-specific database (LSDB) for the allelic sequences of the genes in the HLA system, also known as the human MHC. The IMGT/HLA Database was first released in 1998 and subsequently incorporated as a module of IPD in 2012.
mycoCLAP is a searchable resource for the knowledge and annotation of Characterized Lignocellulose-Active Proteins of fungal origin.
Influenza Research Database
The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization, and comparative genomics analysis, together with personal login- protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.
Human Endogenous Retrovirus database
This database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. The database makes it possible to continuously improve classification and characterization of retroviral families. The HERV database now contains retroviruses from more than 90 % of the human genome.
Implemented the SNP discovery software autoSNP within a relational database to enable the efficient mining of the identified polymorphisms and the detailed interrogation of the data. AutoSNP was selected because it does not require sequence trace files and is thus applicable to a broader range of species and datasets.
Addgene is a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.
Assembling the Fungal Tree of Life
The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life.
AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.
Databases of Orthologous Promoters
DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Based on the Arabidopsis thaliana and Homo sapiens genome annotation, this resource is also a collection of the orthologous promoter sequences from Viridiplantae and Chordata species. The database can be used to find promoter clusters of different genes as well as positions of the conserved regions and transcription start sites, which can be viewed graphically.
Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through the Allergen Data Laboratories via unrestricted grants from companies and institutions.
Evolutionary Annotation Database
Evola contains ortholog information of all human genes among vertebrates. Orthologs are a pair of genes in different species that evolved from a common ancestral gene by speciation. In Evola, orthologs were detected by comparative genomics and amino acid sequence analysis (Computational analysis).
DNASU Plasmid Repository
DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.
The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of information known about telomerase enzyme and its substrate, telomeres.
Mammalian Protein Localization Database
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.
Drosophila polymorphism database
Drosophila Polymorphism Database, is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Drosophila genus. It allows, for the first time, the search for any polymorphic set according to different parameter values of nucleotide diversity.
Relative evolutionary importance of amino acids within a protein sequence.
Beijing Genomics Institute Rice Information System
In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The database has annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified.
Chicken Variation Database
The chicken Variation Database (ChickVD) is an integrated information system for storage, retrieval, visualization and analysis of chicken variation data.
Influenza Virus Database
IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.
Pig Genomic Informatics System
The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed Sequence Tags (ESTs) generated by Sino-Danish Pig Genome Project, and 1 million miscellaneous GenBank records.
YanHuang - YH1 Genome Database
The YH database presents the entire DNA sequence of a Han Chinese individual, as a representative of Asian population. This genome, named as YH, is the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years.assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified.
The Barcode of Life Data Systems
The Barcode of Life Data Systems (BOLD) is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community.
Ciona intestinalis Protein Database
CIPRO is an integrated protein that has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advance and useful information for starting biological and biomedical research. The protein information in CIPRO directly links to gene expression, a tool for peptide mass fingerprinting (PMF), intracellular localization, 3D image of early development, and transgenic resources.
PROkariotIC Database Of Gene-Regulation
PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.
National Microbial Pathogen Data Resource
The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
siRecords is a collection of a diverse range of mammalian RNAi experiments . After choosing a gene, researchers can find all siRNA records targeting the gene, design a new siRNA targeting it, or submit siRNAs that have been tested. The resource also helps experimental RNAi researchers by providing them with the efficacy and other information about the siRNAs experiments designed and conducted previously against the genes of their interest. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.
Human-Transcriptome Database for Alternative Splicing
H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis including genome-wide representative alternative splicing variants (RASVs), RASVs affecting protein functions, conserved RASVs compared with mouse genome (full length cDNAs).
Cnidarian Evolutionary Genomics Database
CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians.
StellaBase is the Nematostella vectensis genomics database.
Tandem Repeats Database
Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA and contains a variety of tools for their analysis.
Comparative Fungal Genomics Platform
The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes.
Magnaporthe grisea Database
The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. The project is a partnership between the International Rice Blast Genome Consortium, and the Broad Institute. The project is facilitated by an Advisory Board made up of members of the rice blast research community.
The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the list of genes. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.
PhosphoSite Plus provides extensive information on mammalian post-translational modifications (PTMs). The resource supersedes PhosphoSite a mammalian protein database that provides information about in vivo phosphorylation sites.
The Chromosome 7 Annotation Project
The objective of this project is to generate the most comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications.
RNAiDB provides access to results from RNAi interference studies in C. elegans , including images, movies, phenotypes, and graphical maps.
Candida Genome Database
The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.
The Database of Human DNA Methylation and Cancer
The database of human DNA Methylation and Cancer (MethyCancer) is developed to study interplay of DNA methylation, gene expression and cancer. It hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing.
Shanghai Rapeseed Database
Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica.
GreenPhylDB: A phylogenomic database for plant comparative genomics
GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.
OryGenesDB: an interactive tool for rice reverse genetics
The aim of this Oryza sativa database was first to display sequence information such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. This information was later linked with related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data...).
Oryza Tag Line
Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.
TropGENE DB is a database that manages genetic and genomic information about tropical crops studied by Cirad. The database is organised into crop specific modules.
Information system for G protein-coupled receptors
The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.
Plant Genome Network
PGN is a repository for plant EST sequence data located at Cornell. It comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project.
Sol Genomics Network
The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.
The DrugBank database is a freely available bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
European Nucleotide Archive
The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
Patent Data Resources
Patent data resources at the EBI contain patent abstracts, patent chemical compounds, patent sequences and patent equivalents. Multiple sets of patent sequences are available at EBI. Patent proteins cover sequences of EPO (European Patent Office) proteins, JPO (Japan Patent Office) proteins, KIPO (Korean Intellectual Property Office) proteins and USPTO (United States Patent and Trademark Office) proteins. Patent nucleotides contain the patent class data in the EMBL-Bank. Non-redundant patent sequences consist of 2 levels databases. Level-1 non-redundant patent sequences are 100% identical over the same length; Level-2 non-redundant patent sequences are identical and belong to a same patent family (a same invention).
Integrated resource of protein families, domains and functional sites
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium.
Ligand-Gated Ion Channel database
The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.
PDBsum; at-a-glance overview of macromolecular structures
PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.
Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.
Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.
Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.
Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.
Expression Database in 4D
This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.
STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.
CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining.
Eukaryotic Pathogen, Vector and Host Informatics Resource
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) focuses on eukaryotic pathogens and invertebrate vectors of infectious diseases, , encompassing data from prior resources devoted to parasitic species (EuPathDB), fungi (FungiDB) and vector species (VectorBase). While each of the taxonomic groups within this resource is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.
A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.
MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.
ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains available for variant detection and copy number variation analysis. In addition to genomic sequence data, ToxoDB contains functional genomic datasets including microarray, RNAseq, proteomics, ChIP-seq, and phenotypic data. In addition, results from a number of whole-genome analyses are incorporated, including mapping to orthology clusters, which allows users to leverage phylogenetic relationships in their analyses.
TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
TriTrypDB is one of the databases that can be accessed through the VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the VEuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
Human Oral Microbiome Database
The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information.
The Gene Index Project
The goal of The Gene Index Project is to use the available EST and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products.
Protein Classification Benchmark Collection
The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.
Interrupted coding sequences
ICDS database is a database containing ICDS detected by a similarity-based approach. The definition of each interrupted gene is provided as well as the ICDS genomic localisation with the surrounding sequence.
The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.
ImMunoGeneTics Information System
IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates.
Annotated regulatory Binding Sites from Orthologous Promoters
ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.
Database of Protein Disorder
The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions are manually curated from literature. DisProt annotations cover both structural and functional aspects of disorder detected by specific experimental methods.
Drosophila Species Genomes
The D. melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species, and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.
euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.
Daphnia Water Flea Genome Database
wFleaBase includes data from all species of the genus, yet the primary species are Daphnia pulex and Daphnia magna, because of the broad set of genomic tools that have already been developed for these animals.
Aphid Genomics Database
The Aphid Genome Database's aim is to improve the current pea aphid genome assembly and annotation, and to provide new aphid genome sequences as well as tools for analysis of these genomes.
SpodoBase is an integrated database for the genomics of the Lepidoptera Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of gene families of interest for the scientific community.
VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.
Buruli ulcer bacillus Database
A database dedicated to the analysis of the genome of Mycobacterium ulcerans, the Buruli ulcer bacillus. It provides a complete dataset of DNA and protein sequences derived from the epidemic strain Agy99, linked to the relevant annotations and functional assignments.
Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.).
GenoList Genome Browser
GenoList is an integrated environment for comparative exploration of microbial genomes. The current release integrates genome data for over 700 species (Genome Reviews). The query and navigation user interface includes specialized tools for subtractive genome analysis and dynamic synteny visualization.
Legionella pneumophila genome database
LegioList is a database dedicated to the analysis of the genomes of Legionella pneumophila strain Paris (endemic in France), strain Lens (epidemic isolate), strain Phildelphia 1, and strain Corby. It also includes the genome of Legionella longbeachae strain NSW150.
Listeria innocua and Listeria monocytogenes genomes database
ListiList is a database dedicated to the analysis of the genomes of the food-borne pathogen, Listeria monocytogenes, and its non-pathogenic relative, Listeria innocua. Its purpose is to collate and integrate various aspects of the genomic information from L. monocytogenes, a paradigm for bacterial-host interactions.
Mycoplasma pulmonis genome database
Its purpose is to collate and integrate various aspects of the genomic information from M. pulmonis, a mollicute causal agent of murine respiratory mycoplasmosis. MypuList provides a complete dataset of DNA and protein sequences derived from the strain M. pulmonis UAB CTIP, linked to the relevant annotations and functional assignments.
Photorhabdus luminescens genome database
PhotoList, contains a database dedicated to the analysis of the genome of Photorhabdus luminescens. This analysis has been described in: "The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens"
Streptococcus agalactiae NEM316 / Serotype III genome database
SagaList contains a database dedicated to the analysis of the genomes of the food-borne pathogen, Streptococcus agalactiae.
Bacillus subtilis strain 168 genome
Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments
The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and sequence and spectral library searches are applied. Analyses are performed to produce a probability of correct identification for all results in a uniform manner, together with false discovery rates at the whole-atlas level.
Bactibase: database dedicated to bacteriocins
BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.
Human Protein Reference Database
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
MycoBank is a database created for the mycological community (as well as scientific community more generally) to document new mycological names, combinations and associated data (such as descriptions and illustrations ). Pairwise sequence alignments and polyphasic identifications of fungi and yeasts against curated references databases are proposed. Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural error. Deposited names can remain confidential until after publication as required. Once public, the names are accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative.
SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.
PSIbase is a molecular interaction database based on PSIMAP (PDB, SCOP) that focuses on structural interaction of proteins and their domains. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.
BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.
Human Unidentified Gene-Encoded large proteins database
HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).
ROdent Unidentified Gene-Encoded large proteins
The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).
Yeast Searching for Transcriptional Regulators and Consensus Tracking
YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.
Protein Model Database
The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.
A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.
Maize Genetics and Genomics Database
MaizeGDB is the maize research community's central repository for genetics and genomics information.
The Global Proteome Machine Database
The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.
The NEW Antirrhinum majus (Snapdragon) genetic and genomic database
Rat Genome Database
The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research.
Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
Conserved Domain Database
The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, NCBI Protein Clusters, TIGRFAM, NCBIfam). NCBI-curated models are organized hierarchically into families, sub- and super-families, and come with annotation of functional sites.
Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
Expressed Sequence Tags database
The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is expected to be completed 2019. Accession.version and GI identifiers will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/
Influenza Virus Resource
Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.
Molecular Modeling Database
The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.
The Protein Database
The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems. Gene comprises sequences from thousands of distinct taxonomic identifiers, ranging from viruses to bacteria to eukaryotes. It represents chromosomes, organelles, plasmids, viruses, transcripts, and millions of proteins.
NCBI Viral Genomes Resource
NCBI Viral Genomes Resource is a collection of virus genomic sequences that provides curated sequence data, related information and tools. It includes all complete viral genome sequences deposited in the International Nucleotide Sequence Database Collaboration (INSDC) databases, i.e. DDBJ, EMBL, and GenBank. Data are organized by viral taxonomy, and reference sequence records (RefSeqs) from one or more genome sequences for each viral species. After a RefSeq has been created for a species, other complete genomes from that same species are indexed as neighbors to the RefSeq.
Organelle Genome Resource
The organelle genomes are part of the NCBI Reference Sequence (RefSeq) project that provides curated sequence data and related information for the community to use as a standard.
Plant Genome Central
The list of plant sequencing projects in this page includes those that have reached the stage where active sequence determination is currently producing, or is expected to produce in the near future, GenBank accessions toward the goal of determining the sequence of that plant genome.
ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.
Reference Sequence Database
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
UniGene gene-oriented nucleotide sequence clusters
Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
UniSTS was a database of sequence tagged sites (STSs), derived from STS-based maps and other experiments. All data from this resource have been moved to the Probe database. You can retrieve all UniSTS records by searching the probe database using the search term "unists[properties]". Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists). If you have any specific questions, please feel free to contact us at email@example.com
UniVec is a database that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination). In addition to vector sequences, UniVec also contains sequences for those adapters, linkers, and primers commonly used in the process of cloning cDNA or genomic DNA.
NIA Mouse cDNA Project
A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells was assembled. The cDNA libraries are freely distributed to the research community, providing a standard platform for expression studies using microarrays.
Rice Genome Annotation Project
This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.
Drug Adverse Reaction Target
A database for facilitating the search for drug adverse reaction target. DART contains information about known drug adverse reaction targets, functions and properties.
Restriction enzymes and methylases database
A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.
Transporter Classification Database
This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information for organisms of all types. As of April. 1, 2021, TCDB consists of 21,114 proteins classified in 16,558 non-redundant transport systems with 1,605 tabulated 3D structures, 19,196 reference citations describing 1,586 transporter families, of which 26% are members of 83 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. The most recent update of the database contents and features include (1) adoption of a chemical ontology for substrates of transporters, (2) inclusion of new superfamilies, (3) a domain-based characterization of transporter families (tcDoms) for the identification of new members as well as functional and evolutionary relationships between families, (4) development of novel software to facilitate curation and use of the database, (5) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators, and (6) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.
The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science.
Homologous Vertebrate Genes Database
HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.
The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
ArachnoServer: Spider toxin database
ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom.
Description of Plant Viruses
DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. The database will not be updated with sequence or taxonomic data from Aug 2013.
TargetTrack, a target registration database, provides information on the experimental progress and status of targets selected for structure determination.
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
Sanger Pfam Mirror
The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.
The Vertebrate Genome Annotation Database
The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.
3D interacting domains
The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur.
Pseudomonas Genome DB
The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.
Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
HAMAP database of microbial protein families
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Type 1 Diabetes Database
T1DBase focuses on two research areas in type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.
Domain mapping of disease mutations
Domain mapping of disease mutations (DMDM) is a database in which each disease mutation can be displayed by its gene, protein or domain location.
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").
A CLAssification of Mobile genetic Elements
ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.
The CATH database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It provides a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor).
The Human Metabolome Database
The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
Toxin and Toxin Target Database
Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.
GpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search.
Xenopus laevis and tropicalis biology and genomics resource
Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically-significant interactions.
Database of Interacting Proteins
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the core DIP data.
VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.
The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation.
Molecular database for the identification of fungi
UNITE is primarily a fungal rDNA internal transcribed spacer (ITS) sequence database, although they also welcome additional genes and genetic markers. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria.
Bacterial Protein Interaction Database
Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.
Poxvirus Bioinformatics Resource Center
Poxvirus Bioinformatics Resource Center has been established to provide specialized web-based resources to the scientific community studying poxviruses. This resource is no longer being maintained. For tools and data supporting virus genomics, especially related to poxviruses and other large DNA viruses, please visit the Viral Bioinformatics site maintained by our collaborator, Chris Upton: http://virology.ca For information on virus taxonomy, please visit the ICTV web site at http://www.ictvonline.org/ For updated sequence data and analytical tools, please visit http://www.viprbrc.org
VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrated resource for the research community. VectorBase contains genome information for organisms such as Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.
Genome Database for Rosaceae
The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.
Yeast Resource Center Public Data Repository
The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.
EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
CentrosomeDB is a collection of human and drosophila centrosomal genes that were reported in the literature and other sources. The database offers the possibility to study the evolution, function, and structure of the centrosome. They have compiled information from many sources, including Gene Ontology, disease-association, single nucleotide polymorphisms, and associated gene expression experiments.
The MOuse NOnCode Lung database
MONOCLdb is an integrative and interactive database designed to retrieve and visualize annotations and expression profiles of long-non coding RNAs (lncRNAs) expressed in Collaborative Cross (http://compgen.unc.edu/) founder mice in response to respiratory influenza and SARS infections.
FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of different levels, from browsing to construction of complex queries, which can be executed on either single items or lists.
MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database features three levels of annotation: manually curated, indirect and predicted. MobiDB annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined.
RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services.
Eukaryotic Promoter Database
The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name “EPDnew”) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq (https://ccg.epfl.ch/chipseq) and Signal Search Analysis (https://ccg.epfl.ch/ssa), for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.
Alternative Poly(A) Sites database
APASdb can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
Catalogue of Somatic Mutations in Cancer
The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.
GrainGenes, a Database for Triticeae and Avena
The GrainGenes website hosts a wealth of information for researchers working on Triticeae species, oat and their wild relatives. The website hosts a database encompassing information such as genetic maps, genes, alleles, genetic markers, phenotypic data, quantitative trait loci studies, experimental protocols and publications. The database can be queried by text searches, browsing, Boolean queries, MySQL commands, or by using pre-made queries created by the curators. GrainGenes is not solely a database, but serves as an informative site for researchers and a means to communicate project aims, outcomes and a forum for discussion.
Proteome-pI : proteome isoelectric point database
Proteome-pI is an online database containing information about predicted isoelectric points for 5,029 proteomes (21 million of sequences) calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography–mass spectrometry and X-ray protein crystallography. The database allows the retrieval of virtual 2D-PAGE plots and the development of customized fractions of proteome based on isoelectric point and molecular weight. Moreover, Proteome-pI facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life (http://isoelectricpointdb.org/statistics.html). The database includes various statistics and tools for interactive browsing, searching and sorting. It can be searched and browsed by organism name, average isoelectric point, molecular weight or amino acid frequencies. Proteins with extreme pI values are also available. For individual proteomes, users can retrieve proteins of interest given the method, isoelectric point and molecular weight ranges (this particular feature can be highly useful to limit potential targets in analysis of 2DPAGE gels or before conducting mass spectrometry). Finally, some general statistics (total number of proteins, amino acids, average sequence length, amino acid and di-amino acid frequencies) and datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated.
Banana Genome Hub
The Banana Genome Hub centralises databases of genetic and genomic data for the Musa acuminata crop, and is the official portal for the Musa genome resources.
BCCM/GeneCorner Plasmid Collection
The BCCM/GeneCorner Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance. The focus is on the collection of recombinant plasmids that can replicate in a microbial host strain. BCCM/GeneCorner also accepts natural and genetically modified animal or human cell lines, including hybridomas, as well as other genetic material, in the safe deposit and patent deposit collections.
LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.
Hardwood Genomics Project
The Hardwood Genomics Project is a databases for expressed genes, genetic markers, genetic linkage maps, and reference populations. It provides lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for growth, adaptation and responses to environmental stresses such as drought, heat, insect pests and disease. All original sequence data is being deposited in NCBI's Sequence Read Archive and the genetic linkage maps and associated marker data will be available at the Dendrome database.
The Triticeae Toolbox
The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Agriculture (USDA). The current project is funded through NIFA's International Wheat Yield Partnership (IWYP) and part of the Agriculture and Food Research Initiative (AFRI).
Visual Database for Organelle Genome
VDOG, Visual Database for Organelle Genome is an innovative database of the genome information in the organelles. Most of the data in VDOG are originally extracted from GeneBank, re-organized and represented.
Small angle scattering biological data bank
Curated repository for small angle scattering data and models. SASBDB contains X-ray (SAXS) and neutron (SANS) scattering data from biological macromolecules in solution.
Vertebrate Secretome Database
Vertebrate Secretome Database (VerSeDa) stores information about proteins that are predicted to be secreted through the classical and non-classical mechanisms, for the wide range of vertebrate species deposited at the NCBI, UCSC and ENSEMBL sites.
Regulatory Element Database for Drosophila
REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct.
iGEM Registry of Standard Biological Parts
The iGEM Parts Registry is a growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. As part of the synthetic biology community's efforts to make biology easier to engineer, it provides a source of genetic parts to iGEM teams and academic labs. You can learn more about iGEM Teams and Labs at iGEM.org.
WALTZ-DB 2.0 is a database for characterizing short peptides for their amyloid fiber-forming capacities. The majority of the data comes from electron microscopy, FTIR and Thioflavin-T experiments done by the Switch lab. Apart from that class of data we also provide the amyloid annotation for several other short peptides found in current scientific research papers. Structural models of the potential amyloid cores are provided for every peptide entry.
PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching.
rPredictorDB is a predictive database of secondary structures of individual RNAs and their formatted plots.
T-psi-C is a database of tRNA sequences and 3D tRNA structures. The T-psi-C database can be continuously updated by any member of the scientific community.
GlyGen: Computational and Informatics Resources for Glycoscience
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone.
InterMine was formed in 2002 at the University of Cambridge, originally as a Drosophila-dedicated resource, before expanding to become organism-agnostic, enabling a large range of organisations around the world to create their own InterMines. There are many instances of InterMine installations, relating to particular model organisms. These can be searched individually or via a cross-Mine search function.
Genome Variation Map
The Genome Variation Map (GVM) is a public data repository of genome variations, including single nucleotide polymorphisms (SNP) and small insertions and deletions (INDEL), with particular focuses on human as well as cultivated plants and domesticated animals. GVM collects, integrates and visualizes genome variations for a wide variety of species, accepts submissions of different types of genome variations from all over the world and provides open access for all publicly available data. Based on a large collection of raw sequence data from public repositories, GVM integrates a large number of genome variants for a number of species and provides web interfaces for data submission, search, browse and visualization.
Information Commons for Rice
Information Commons for Rice (IC4R) is a rice knowledgebase that incorporates rice data through multiple modules such as genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community.
piRBase stores information on piRNAs and piRNA-associated data to support piRNA functional analysis.
Kinase-Ligand Interaction Fingerprints and Structures database
Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and consistent protocol all (currently human and mouse) kinase structures and the binding mode of kinase ligands can be directly compared to each other. Moreover, because of the classification of an all-encompassing binding site of 85 residues it is possible to compare the interaction patterns of kinase-inhibitors to each other to, for example, identify crucial interactions determining kinase-inhibitor selectivity.
DDBJ Sequence Read Archive
DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA).
Genomic Observatories Meta-Database
The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.
RNA Atlas of Structure Probing
RASP (RNA Atlas of Structure Probing) is build from 161 deduplicated transcriptome-wide RNA secondary structures from datasets culled from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. Specially, RASP curates the up-to-date datasets of several RNA secondary structure probing studies for the RNA genome of SARS-CoV-2, the RNA virus that caused the on-going COVID-19 pandemic. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data.
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National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
United States Department of Health and Human Services (Government body)