Hello Tomas, There is a previously answered mailing list question that will solve 1/3 of your problem, regarding PFAM here: https://lists.soe.ucsc.edu/pipermail/genome/2008-January/015315.html
It describes the relationship between a ucsc genes gene name, and a pfam name, using the table knownToPfam. From there, you can get the coordinates of the ucsc gene through the table knownGene. Try a query like this, and edit to include the columns you're interested in: mysql> select knownToPfam.name, knownToPfam.value, knownGene.name, knownGene.chrom, knownGene.cdsStart, knownGene.cdsEnd from knownToPfam join knownGene on knownToPfam.name = knownGene.name limit 10; For the SMART data, I don't believe we have a representation of that dataset in the Genome Browser. The Superfamily data was supported in the Genome Browser at one time, but is no longer, unfortunately. I hope this helps to get you started. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "Tomas Babak" <[email protected]> wrote: > Hi, > > I am a frequent user of the UCSC browser suite of tools. I'm trying > to > accomplish what several threads seem to have attempted to address but > without a resolution: > > Construct a track of PFAM, SMART, and SCOP/Superfamily domains in > genomic coordinates for the human genome. > > I can convert between protein and genomic coordinates but cannot find > any tables that have coordinates for protein domains. At least the > superfamily table must exist somewhere since it is a part of the > proteome browser. I cannot find it under hg18 -> All tables -> > proteome. > Where is it? And does a PFAM and/or SMART table with coordinates > exist? > > Any help or advice would be much appreciated. > > Tomas > > > > _______________________ > > > Tomas Babak > Senior Research Scientist > MRL Boston > 617-992-2554 > > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact > information for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended > solely for the use of the individual or entity named on this message. > If you are not the intended recipient, and have received this message > in error, please notify us immediately by reply e-mail and then delete > it from your system. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
