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a catalog of biological databases

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Database information

UCSC Archaeal Genome Browser

General information

Description: 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.
Year founded: 2006
Last update:
Version:
Accessibility:
Manual:
Accessible
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Country/Region: United States
Data type:
Data object:
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Major organism:
NA
Keywords:

Contact information

University/Institution: University of California Santa Cruz
Address: Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA
City: Santa Cruz
Province/State: California
Country/Region: United States
Contact name (PI/Team): Todd M. Lowe
Contact email (PI/Helpdesk): lowe@soe.ucsc.edu

Record metadata

Created on: 2018-01-29
Curated by:
Nashaiman Pervaiz [2018-12-28]
pei wang [2018-03-06]

Ranking

All databases:
748/4549 (83.579%)
Gene genome and annotation:
256/1211 (78.943%)
748
Total Rank
129
Citations
9.214
z-index

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Publications

22080555
The UCSC Archaeal Genome Browser: 2012 update. [PMID: 22080555]
Chan PP, Holmes AD, Smith AM, Tran D, Lowe TM.

The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 archaeal genomes, plus 31 genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available archaeal genomes.

Nucleic Acids Res. 2012:40(Database issue) | 49 Citations (from Europe PMC, 2020-02-08)
16381898
The UCSC Archaeal Genome Browser. [PMID: 16381898]
Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM.

As more archaeal genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human genome, can be applied to any sequenced organism. We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 archaeal genomes. It displays G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments and protein conservation across phylogenetic and habitat categories. We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community.

Nucleic Acids Res. 2006:34(Database issue) | 80 Citations (from Europe PMC, 2020-02-08)