Aligning Genomic Regions Of Proteins

Question

[Pappu]

I want to compare the genomic organization (exons and intros) of two similar proteins. I am wondering which tool will be suitable for this purpose.

Answer 1

[Andrzej Zielezinski]

I use Exonerate for this.

It's very simple to run it:

exonerate query.fasta target.fasta

It guesses, by deafult, which inputs are DNA and which are proteins.

Answer 2

[Gabriel R.]

have you tried TBLASTN ? You can parse your exon hits as a post-processing step.