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
