I am planning to compare introns of a specific gene in various species, in order to detect intron loss or gain. I believe multiple sequence alignment is the best way to do so. In addition, I do have the entire gene sequences of the organisms in consideration, with their exon and intron coordinates clearly mentioned. However, I just want to exclude exons from my alignment. I'm not sure if removing all exons and joining the introns in a single string, would be an efficient way or not.
Also, which tool would give me the best representation of intron loss/gain ?
Your advice will be highly appreciated.
The best way would be to include whole genomic sequences (intron +exon) and perform multiple sequence analyses (MSA). Prior to that note down the start and end positions of all exons in each submitted sequence. After MSA, wherever you find differences you may find out whether that change is in its intronic or exonic region. Hope it helps!!
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