Identifying truncated protein domain encoding DNA sequences

Question

[Anand Rao]

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:

1. the encoded protein domain is partial or truncated, and / or
2. the encoding region may be interrupted by one or more introns, and
3. 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!