Exon Match/ Genome parser

[danjg]

Greetings all,

I'm working on digging out some conserved sites from a transcriptome of the non model group that I work on (a close relative to tomato and potato) and my objective was to look for conserved regions flanked by non-conserved regions to find areas with 1.) conserved regions to tile target enrichment baits over and 2.) variable flanking regions of phylogenetic utility (likely intron / non coding).

To accomplish this I'd like to blast my transcriptome to the tomato and potato genomes and be able to see where my transcripts line up with the two (like in a blast alignment, i.e. blastall -m 3) as well as all the tomato/potato regions around those areas (as a way of assessing the variability in the flanking introns). Has anyone encountered a problem like this before? Ideally I would end up with the hit from my organism and tomato/potato + maybe a 2,000 base alignment of tomato/potato on either side of that hit

I feel like there should be a way of doing this without all the coding I'm attempting

[TiborNagy]

If your organism can be found on EnsEMBL plant, maybe you can use EnsEMBL API to fetch the multiple alignments or you can use other annotations. If it is an unique plant, you need to code a lot.

[danjg]

hrm, that's what I thought, at least lots of python and linux scripts didn't go to waste. Thanks for the response Tibor!