Is there an off-the-shelf tool or pipeline that will report all protein domain encoding DNA encoding sequences in a given genome, INCLUDING these conditions:
- the encoded protein domain is partial or truncated, and / or
- the encoding region may be interrupted by one or more introns, and
- has the flexibility of using protein profile as query to scan the genome.
I have some amorphous ideas about using fastBlockSearch in AUGUSTUS, and / or PseudoPipe. But I am collecting better crystallized ideas, especially if you've already solved this problem.
Thank you, in advance. Cheers!