Thu, 21 Aug 2008 00:44:57 BST CiteULike: miguel's Karolchik http://www.citeulike.org/user/miguel/author/Karolchik CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/miguel/article/1138879 <i>Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)</i><br /><br />The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/. The UCSC genome browser database: update 2007. RM Kuhn D Karolchik AS Zweig H Trumbower DJ Thomas A Thakkapallayil CW Sugnet M Stanke KE Smith A Siepel KR Rosenbloom B Rhead BJ Raney A Pohl JS Pedersen F Hsu AS Hinrichs RA Harte M Diekhans H Clawson G Bejerano GP Barber R Baertsch D Haussler WJ Kent Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) 2007-03-03T23:15:02-00:00 2007 Nucleic Acids Res 1362-4962 35 Database issue browser genome ucsc http://www.citeulike.org/user/miguel/article/514551 <i>Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)</i><br /><br />The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/. The UCSC Genome Browser Database: update 2006. AS Hinrichs D Karolchik R Baertsch GP Barber G Bejerano H Clawson M Diekhans TS Furey RA Harte F Hsu J Hillman-Jackson RM Kuhn JS Pedersen A Pohl BJ Raney KR Rosenbloom A Siepel KE Smith CW Sugnet A Sultan-Qurraie DJ Thomas H Trumbower RJ Weber M Weirauch AS Zweig D Haussler WJ Kent Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) 2006-02-21T15:18:40-00:00 2006 Nucleic Acids Res 1362-4962 34 Database issue database est genome http://www.citeulike.org/user/miguel/article/312767 <i>Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)</i><br /><br />The University of California Santa Cruz (UCSC) Table Browser (http://genome.ucsc.edu/cgi-bin/hgText) provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database. A flexible alternative to the graphical-based Genome Browser, this tool offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries and combined queries on multiple tables. Output can be filtered to restrict the fields and lines returned, and may be organized into one of several formats, including a simple tab- delimited file that can be loaded into a spreadsheet or database as well as advanced formats that may be uploaded into the Genome Browser as custom annotation tracks. The Table Browser User's Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output. The UCSC Table Browser data retrieval tool. D Karolchik AS Hinrichs TS Furey KM Roskin CW Sugnet D Haussler WJ Kent Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004) 2005-09-07T18:29:23-00:00 2004 Nucleic Acids Res 1362-4962 32 Database issue database genome