title: The UCSC Archaeal Genome Browser: 2012 update.
abstract: 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.
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA.
authors.forename: Patricia P
authors.initials: PP
authors.lastname: Chan
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Holmes
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Smith
authors.forename: Danny
authors.initials: D
authors.lastname: Tran
authors.forename: Todd M
authors.initials: TM
authors.lastname: Lowe
mesh_terms: D001105:Archaea / Q000821:virology; D019843:Archaeal Proteins / Q000235:genetics; D030541:Databases, Genetic; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016679:Genome, Viral; D020407:Internet; D058977:Molecular Sequence Annotation; D019642:RNA, Archaeal / Q000737:chemistry
chemical_list: D019843:Archaeal Proteins; D019642:RNA, Archaeal
references.citation: BMC Bioinformatics. 2003 Sep 11;4:41
references.pmid: 12969510
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
references.pmid: 14681465
references.citation: Genome Res. 2002 Jun;12(6):996-1006
references.pmid: 12045153
references.citation: Mol Biol Evol. 2010 Oct;27(10):2233-43
references.pmid: 20430862
references.citation: J Comput Biol. 2004;11(2-3):413-28
references.pmid: 15285899
references.citation: BMC Bioinformatics. 2010 Mar 08;11:119
references.pmid: 20211023
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Cell. 2009 Nov 25;139(5):945-56
references.pmid: 19945378
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D32-6
references.pmid: 16381877
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D382-90
references.pmid: 19864254
references.citation: Bioinformatics. 2010 Sep 1;26(17):2204-7
references.pmid: 20639541
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5
references.pmid: 21062808
references.citation: Bioinformatics. 2007 Mar 15;23(6):673-9
references.pmid: 17237039
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D479-82
references.pmid: 18948284
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
references.pmid: 17130148
references.citation: Genome Biol. 2011;12(4):R38
references.pmid: 21489296
references.citation: Nucleic Acids Res. 2001 Jun 15;29(12):2607-18
references.pmid: 11410670
references.citation: BMC Bioinformatics. 2007 Jun 18;8:209
references.pmid: 17577412
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7
references.pmid: 21071399
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
references.pmid: 16381885
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9
references.pmid: 21109532
references.citation: Genome Res. 2005 Aug;15(8):1034-50
references.pmid: 16024819
references.citation: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references.pmid: 9023104
references.citation: Genome Res. 2004 Apr;14(4):708-15
references.pmid: 15060014
references.citation: Nature. 2005 Feb 3;433(7025):537-41
references.pmid: 15690044
references.citation: J Bacteriol. 2009 Feb;191(3):782-94
references.pmid: 19047344
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7
references.pmid: 18984615
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
references.pmid: 18045790
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7
references.pmid: 17537822
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9
references.pmid: 19906737
references.citation: Genome Biol. 2010;11(8):R86
references.pmid: 20738864
references.citation: Science. 1997 Oct 24;278(5338):631-7
references.pmid: 9381173
references.citation: Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2683-7
references.pmid: 19190180
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5
references.pmid: 19892825
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10
references.pmid: 21097893
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54
references.pmid: 18948282
references.citation: Nucleic Acids Res. 2005 Feb 08;33(3):880-92
references.pmid: 15701760
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D407-10
references.pmid: 16381898
references.citation: RNA. 2003 Dec;9(12):1516-31
references.pmid: 14624007
references.citation: Biol Direct. 2007 Nov 27;2:33
references.pmid: 18042280
references.citation: J Bacteriol. 2007 Jun;189(12):4431-41
references.pmid: 17449625