Hello Tar, Please see this previously answered mailing list question:
https://lists.soe.ucsc.edu/pipermail/genome/2011-November/027780.html Basically you will want to use our blastTab tables (in this case the mmBlastTab table) which maps UCSC genes identifiers from one assembly to another. You will also need to use a linked table (kgXref) to convert your Uniprot identifiers to UCSC genes identifiers. Note that Uniprot identifiers are equivalent to " SWISS-PROT protein Accession numbers" in the kgXref table, so begin by choosing that table (as outlined in the link above), then you will be able to paste in your Uniprot identifiers as a list. Then choose "selected fields from primary and related tables" click "get output" and in the subsequent menu be sure to check the "mmBlastTab" table and "allow selection from checked tables". This will allow you to include fields from the mmBlastTab table in your output and you will want to include the query (human id) and target (mouse id) fields. To convert the resulting list of mouse UCSC ids back to Uniprot you would need to use the kgXref a second time pasting in the list of UCSC ids and then selecting the "SWISS-PROT protein Accession numbers" field for your output. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 1/11/12 8:56 AM, Tar Viturawong wrote: > Hello, > > I'm trying to compare interaction data between two organisms: mouse and > human and working with Uniprot identifiers, and I'm wondering whether there > is a way to map a set of Uniprot identifiers as homologs of another set? > For example, is there perhaps a way to download some sort of table that > contains information linking pairs of gene identifiers, one from mouse and > one from human, as homologs? I have a feeling it might be a far-fetched > request but I thought I'd give it a try. If the Genome Browser isn't the > right place for this, could anyone suggest where I could continue looking? > > Many thanks! > Tar > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
