Hi Tom, Thomas Juettemann's suggestion of using the pfam website for what you're looking to do seems appropriate. We do have pfam information in relation to our UCSC Genes track that can be downloaded via the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), but your results would be limited by the strict criteria we use to create the UCSC Genes track. In the table browser, the table you would select would be the knownGenes table (the primary UCSC Genes table) and you would also get info from fields in these related tables: knownToPfam and pfamDesc (you'd see an option to get fields from related tables if you choose "selected fields from primary and related tables" as your output). You would then create a filter of these based on pfamDesc.description field for each protein family, e.g.*protease*.
For more information about using the Table Browser, see the Open Helix table browser training video (http://www.openhelix.com//cgi/tutorialInfo.cgi?id=28) and the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. Please contact the mail list ([email protected] <mailto:[email protected]>) again you decide you would like to do the table browser query that I briefly described above and need more specific instructions. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Tom Traut wrote, On 04/01/11 11:34: > Can I use your site (or any other) to find a listing of major protein > families? > > how many kinases > how many proteases > how many G proteins > > etc > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
