Hi, Mary,
I tried to collect fasta sequences from multiz46way, and run clustalw together with the orthologous sequences from other lower species (c. elegans, drosophila, yeast, etc). Somehow, the multiple alignment results aren't as good as multiz46way. I guess I need to tune some parameters in clustalw to make it work better. At the same time, could you please give me some suggestions on how to do it with the genome browser tools, which are used by you to build its multiz46way? Also, is Genome Browser gonna expand its current multiz46way to cover lower species, in addition to the 46 vertebrates? Thanks Sean -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Mary Goldman Sent: Wednesday, June 08, 2011 2:47 PM To: Michael Lush Cc: [email protected] Subject: Re: [Genome] Orthology assertions for HCOP 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
