Hello, A few more suggestions were made by some of the scientists here:
1) Examine the Conservation track. It has multiple alignments at the genomic level, but if you had a region of interest, it would reveal the conserved region in another species (that is part of the 44-way group), whether a gene had been defined in that genome yet (or should be defined) or not. 2) Also, if you would like the data as an output file (not just to view in the browser), from the Table browser one of the output types will return multiple amino acid alignments. First select a "Gene and Gene predictions" track as your base (perhaps filtered by ID or region), then choose "CDS FASTA " from the output menu, then pick a MAF file (Conservation, etc) to output for the genomic regions covered by the filtered Gene track. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Miriam Meisler" <[email protected]> > Cc: [email protected] > Sent: Friday, September 18, 2009 10:03:08 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] species alignment of amino acid sequences > > Hello, > > Yes. There are tracks in the browser that already contain this type of > data or you can upload alignment data in a format called MAF using the > Custom Track feature. > > For example, in the Human March 2006 (hg18) assembly, open the track > called "Other RefSeq" as full, click on the track name to go the > details page and set "Color track by codons:" to "genomic codons", and > then zoom down to the AA level at exon locations. There are also > tracks called "Other mRNAs" and "Other ESTs" with various types of > color coding (see each track for the options). > > Not all species have these "Other" tracks, although many non-human > species do have an alternative track called "Human Proteins" that you > may be interested in. > > For Custom Tracks using MAF format, here are some links to the help > pages: > http://genome.ucsc.edu/cgi-bin/hgCustom > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > http://genome.ucsc.edu/FAQ/FAQformat.html#format5 > > We hope this helps. > Jennifer Jackson > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Miriam Meisler" <[email protected]> wrote: > > > From: "Miriam Meisler" <[email protected]> > > To: [email protected] > > Sent: Friday, September 18, 2009 8:00:48 AM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] species alignment of amino acid sequences > > > > Is it possible to view a multi-species alignment of > > amino acid sequences for a protein using the browser? > > > > > > -- > > Miriam Meisler, Ph. D. > > Department of Human Genetics > > University of Michigan > > 4909 Buhl Box 0618 > > Ann Arbor, MI 48109-0618 > > tel. 734 763 5546 FAX 734 763 9691 > > _______________________________________________ > > 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
