Hi, I think my question is pretty trivial and has probably been raised many times before, nevertheless I couldn't find a direct answer for it in the archives.
Anyway, I'm interested in building Human-Chimp-Orangutan-Rhesus multiple sequence alignments for every human refseq gene. The way I thought of accomplishing this is to: 1. Derive the coding sequence coordinates from the hg19 refGene file for every human refseq gene. 2. Get the sequences of human and each of the other organisms that map to these coordinates from the syntenicNet pairwise alignment files (e.g., chr1.hg19.panTro2.synNet.axt.gz). 3. Combine these pairwise sequence files to multiple sequence files and run my own multiple sequence alignment program. Does this make sense or is there any other better established way to do that? Thanks a lot, Nimrod Rubinstein NESCent fellow _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
