Hello, Yes, use the Table browser and the UCSC Genes track with the identifiers filter. If you upload gene names, all associated transcripts (varients) will be retrieved. You can download or save as a custom track or send to Galaxy. To link back a transcript name (a distinct name we assign with the track) to a gene symbol, use the table kgAlias along with the primary table knownGene. Other tables may also contain information you are interested in - clusters are defined in knownIsoforms and the "representative" transcript for any cluster (i.e. gene) is in knownCanonical. Use the "view schema" link in the browser to examine related tables and the output format "selected fields from primary and related tables" to merge data from linked tables.
Table browser help: http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html We hope this helps you to get started, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Vesselin Baev" <[email protected]> wrote: > From: "Vesselin Baev" <[email protected]> > To: [email protected] > Sent: Monday, December 14, 2009 9:53:07 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] transcript variants alignment > > Dear all, > if I have a list of hundreds of genes, can I retrieve information of > an > alignment for all variants of the gene via Table browser /or Galaxy/? > > Thanks > > -- > ------------------------------------------------ > Dr. Vesselin Baev > Research Assistant Professor > University of Plovdiv > Dept. Molecular Biology > Bioinformatics Group > Tzar Assen 24 > Plovdiv 4000, BULGARIA > +359 32 261 (560) > +359 89 43 80 945 > Skype: vebaev > [email protected] > [email protected] > CV: http://plantgene.eu/vebaev > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
