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UCSC Archaeal Genome Browser


NAR Molecular Biology Database Collection entry number 876
Patricia P. Chan, Andrew D. Holmes, Andrew M. Smith, Danny Tran and Todd M. Lowe
Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA

Database Description

Now that a significant number of archaeal species have been sequenced, effective research and analysis tools are needed to collect and compare the diverse information available for any given locus. We have created a group of integrated genome browsers for all sequenced archaeal species using the feature-rich UCSC Genome Browser system. The browser flexibly displays any combination of features such as G/C content, gene and operon annotation from multiple sources, sequence motifs (i.e., promoters, Shine-Dalgarno, terminators), protein domains, non-coding RNA analyses, GO/COG/KEGG classification information, microarray expression data, multi-genome alignments, and protein conservation across phylogenetic and habitat categories. We continue to add new analyses, both generated within our group as well as those published by other groups. We strongly encourage submission of experimental and bioinformatic analyses from new contributors. The primary aims of this tool are to aid biological discovery and facilitate greater collaboration among the archaeal research community.

Acknowledgements

We thank Jim Kent and the entire Genome Bioinformatics Group of UC Santa Cruz for providing the UCSC Genome Browser and assisting us in developing the Archaeal Genome Browser. Lowe lab members P Chan, M Pearson, and M Weirauch helped develop annotation tracks. Thanks also to Pernille Nielsen of the Krogh lab for contributing the EasyGene gene prediction track.


Go to the abstract in the NAR 2012 Database Issue.
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