Hey all,
I'm investigating are relatively small set of genes, and want to check their presence, and possible pseudogenization in a subset of genomes (cetaceans in my case). My idea is to take known transcript of the gene of interest in human (best annotated), and pig and/or cow (relatively well annotated, and relatively closely related to cetaceans), and align it to the reference genomes of cetaceans. Then I would look at the alignment to see if there are possible frameshifts, premature stopcodons etc...
However, I'm struggling to find good tools to do this. I started by just a simple blast of the transcript against the genome, to see if, and where the transcript is roughly found. Then I extract the sequence where there is a hit, with some extra (5000 bp on each end). Then I want to do an intron/exon aware alignment of the transcript to the extracted sequence. I had a look at Exonerate, and it seems to produce nice alignment, but it doesn't produce a nice alignment format (that I found).
Thus I'm looking for a tool that can create splice-aware alignments of a transcript to a genome, and create an alignment output that is easy to load into an alignment viewer (e.g. MEGA or JalView).
Any ideas?
