Hi Michael, The knownBlastTab table shows the relationship of human genes to other human genes; it is used by the Gene Sorter when you select "sort by Protein Homology - BLASTP": http://genome.ucsc.edu/cgi-bin/hgNear.
The other blastTab tables, which list orthologous genes between species, are only made between each of the following species (as you have noted): human, mouse, rat, C. elegans, drosophila, S. cerevisiae and zebrafish. It is possible to calculate these tables for other species using programs in our source tree: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, however, it is a complicated and involved process. Information on how the blastTab tables are generated can be found in our source tree in src/hg/makeDb/doc/blastTab.txt. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/9/11 2:21 AM, Michael Lush wrote: > > > I had a poke round and noticed this > > ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/knownBlastTab.txt.gz > > > > is it a human to all species ortholog file or is that too easy:-) > > -- > Michael > > > On Wed, 8 Jun 2011, Mary Goldman wrote: >> Hi Michael, >> >> I believe you are asking about our multiz alignments here: >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/. Note >> that this is the alignment of other species' entire assemblies to >> human (hg19), not just a list of genes and their orthologs. >> >> I hope this information is helpful. Please feel free to contact the >> mail list again if you require further assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 6/7/11 4:41 AM, Michael Lush wrote: >>> >>> I currently download orthology assertionf between human and >>> C. elegans, drosophila, mouse, rat, S. cerevisiae and zebrafish >>> from ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes >>> for our HCOP service (www.genenames.org/hcop) >>> >>> I understand that there are orthology assertions from human to other >>> species in your database I'm currently looking at adding new species to >>> the search (and adding extra support to existing ones) and I was >>> wondering >>> how to access this data. >>> >>> -- >>> Michael >>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> Michael John Lush PhD Tel:44-1223 492626 >>> Bioinformatician >>> HUGO Gene Nomenclature Committee Email: [email protected] >>> European Bioinformatics Institute >>> Hinxton, Cambridge >>> URL: http://www.genenames.org >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
