I was looking for somthing more akin to ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/mmBlastTab.txt.gz
ie a set of UCSC ID pairs with one human and the other was the orthologous gene from (species). For HCOP we collect orthology assertions for 14 species from 11 databases and convert them to entrez gene IDs and combine them to determine the consensus view. You have files of pariwise assertions for human to C. elegans, drosophila, mouse S. cerevisiae and zebrafish I was told that it was possible to generate more of these from the database. -- 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
