HMMER Profile File Format
Homepage http://www.hmmer.org
Countries that developed this resource European Union , United Kingdom , United States
Created in 1993
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Feb 28 2021 1:30 p.m.
Publication for citation HMMER web server: 2015 update. Finn RD,Clements J,Arndt W,Miller BL,Wheeler TJ,Schreiber F,Bateman A,Eddy SR; Nucleic Acids Res ; 2015; 10.1093/nar/gkv397;
Record updated: Jan. 17, 2019, 11:15 a.m. by The FAIRsharing Team.
blog | HMMER Blog |
online documentation | Publications |
online documentation | HMMER Documentation |
Additional Information
Contact | Robert D Finn |
TeSS training resources
Similarity searching, multiple sequence alignment and protein families - undergraduate lab
No XSD schemas defined
Conditions of Use
Data Release
HMMER Algorithm Releases | http://www.hmmer.org/download.html |
Data Access
HMMER Homology Search | https://www.ebi.ac.uk/Tools/hmmer/ |
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
Wistrand M,Sonnhammer EL
BMC Bioinformatics 2005
HMMER web server: 2015 update.
Finn RD,Clements J,Arndt W,Miller BL,Wheeler TJ,Schreiber F,Bateman A,Eddy SR
Nucleic Acids Res 2015
Reporting Guidelines
No guidelines defined
Terminology Artifacts
No semantic standards defined
Models and Formats
No syntax standards defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
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.
Type IV Secretion system Resource
A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.
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.
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Record Maintainer
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Funds
The Wellcome Trust, UK (Charitable foundation)
European Commission under FP7 Grant Agreement (Government body)
Maintains
Harvard University, Cambridge, MA, USA (University)
Howard Hughes Medical Institute (Research institute) Lead
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)
Grant Number(s)
108433/Z/15/Z (The Wellcome Trust, UK)