Good Evening Anton: You can fetch a beta release set of MAF files for a 60-species alignment on Mouse/GRCm38/mm10 from our test server:
http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/multiz60way/maf/ Or the 46 species alignment MAF files from Human/GRCh37/hg19: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf/ Beware, these are gigantic files. With these MAF files, a bed file of your specific regions and the kent program mafsInRegion, you can obtain the sequence out of these files. It is not perfectly in multi Fasta format, but it is close enough for a simple transformation. --Hiram > mafsInRegion - Extract MAFS in a genomic region > usage: > mafsInRegion regions.bed out.maf|outDir in.maf(s) > options: > -outDir - output separate files named by bed name field to outDir > -keepInitialGaps - keep alignment columns at the beginning and of a > block that are gapped in all species On 7/19/12 10:07 PM, Anton Kratz wrote: > Dear UCSC team, > > I have a list of a couple of thousand exons or regions on the rat (rn4) > genome defined as start-end coordinates in bed format. These regions are > not in RefSeq, RGD or elsewhere, they are novel determined by me. I want to > check for coding/noncoding poteintial with phyloCSF ( > https://github.com/mlin/PhyloCSF/wiki/). > > Is there any way how I programmatically can get multi-genome alignment for > my regions, in FASTA-format? Ideally for the 29 mammals phylogeny but any > other multi-alignment containing mammals is fine too. > > I was searching around in the data at UCSC provided in context of the 29 > mammals (http://genomewiki.cse.ucsc.edu/index.php/29mammals) project, but > can't find the actual multi-fasta alignment. > > Thanks. > > Anton > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
