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The UCSC Archaeal Genome Browser

General Information

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.

Homepage http://archaea.ucsc.edu

Countries that developed this resource United States

Created in 2005

Taxonomic range

Archaea

Plasmodium falciparum

Knowledge Domains

Subjects

User-defined Tags

Palindromic transcription factor (TF) binding site predictions

Poly T motifs as possible transcription termination signals

How to cite this record FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Apr 08 2020 5:25 a.m.

Record updated: Nov. 21, 2018, 11:02 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.12yd2z' by 'The FAIRsharing Team' at 11:02, 21 Nov 2018 (not approved):

	'domains' has been modified:
		Before:
			CRISPR
			DNA sequence data
			GC content
			Gene expression data
			Gene functional annotation
			Genome map
			Insertion sequence
			Life Science
			Multiple sequence alignment
			Non-coding RNA (ncRNA)
			Nucleic acid sequence alignment
			Operon prediction
			Orthologous
			Palindromic transcription factor (TF) binding site predictions
			Paralogous
			Poly T motifs as possible transcription termination signals
			Prediction and recognition
			Promoter
			RNA sequence
			Sequence annotation
			Transcription factor (TF) binding site prediction
		After:
			CRISPR
			Computational predictions
			DNA sequence data
			GC content
			Gene expression data
			Gene functional annotation
			Genome map
			Insertion sequence
			Life Science
			Multiple sequence alignment
			Non-coding RNA (ncRNA)
			Nucleic acid sequence alignment
			Operon prediction
			Orthologous
			Palindromic transcription factor (TF) binding site predictions
			Paralogous
			Poly T motifs as possible transcription termination signals
			Promoter
			RNA sequence
			Sequence annotation
			Transcription factor (TF) binding site prediction
		Added:
			Computational predictions
		Removed:
			Prediction and recognition

Edits to 'https://fairsharing.org/FAIRsharing.12yd2z' by 'The FAIRsharing Team' at 10:56, 21 Nov 2018 (not approved):

	'domains' has been modified:
		Before:
			CRISPR
			GC content
			Gene expression data
			Gene functional annotation
			Genome map
			Insertion sequence
			Life Science
			Multiple sequence alignment
			Non-coding RNA (ncRNA)
			Nucleic acid sequence alignment
			Operon prediction
			Orthologous
			Palindromic transcription factor (TF) binding site predictions
			Paralogous
			Poly T motifs as possible transcription termination signals
			Prediction and recognition
			Promoter
			RNA sequence
			Sequence annotation
			Transcription factor (TF) binding site prediction
		After:
			CRISPR
			DNA sequence data
			GC content
			Gene expression data
			Gene functional annotation
			Genome map
			Insertion sequence
			Life Science
			Multiple sequence alignment
			Non-coding RNA (ncRNA)
			Nucleic acid sequence alignment
			Operon prediction
			Orthologous
			Palindromic transcription factor (TF) binding site predictions
			Paralogous
			Poly T motifs as possible transcription termination signals
			Prediction and recognition
			Promoter
			RNA sequence
			Sequence annotation
			Transcription factor (TF) binding site prediction
		Added:
			DNA sequence data
		Removed:

Support

General

FAQ	http://archaea.ucsc.edu/FAQ/
help	http://archaea.ucsc.edu/goldenPath/help/ ...
rss	http://archaea.ucsc.edu/feed/

Additional Information

Contact

Todd M. Lowe

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Data Versioning

versioning by NCBI RefSeq genome release date	No link recorded
access to historical files available on request	No link recorded

Data Release

ad-hoc release

No link recorded

Data Curation

automated curation

No link recorded

Data Access

file download(CSV,txt,tab-delimited)	No link recorded
browse	http://archaea.ucsc.edu/genomes/

Publications

The UCSC Archaeal Genome Browser.

Schneider KL., Pollard KS., Baertsch R., Pohl A., Lowe TM.,
Nucleic Acids Res. 2006

View Paper (PubMed) View Publication

The UCSC Table Browser data retrieval tool.

Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ.,
Nucleic Acids Res. 2004

View Paper (PubMed) View Publication

BLAT--the BLAST-like alignment tool.

Kent WJ.,
Genome Res. 2002

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

No related databases defined

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

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Funds

National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)

Maintains

The UCSC Archaeal Genome Browser

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