Identification of protein domain encoding multi-exon genomic intervals

Question

[Anand Rao]

My goal is NOT to discover and report full length genes from a target genome

BUT

to discover in a genome of interest,

1. intervals that code only for a protein domain of interest,
2. where the protein domain is defined by it's Pfam ID (profile HMM), and
3. where the domain encoding is always multi-exonic.

Unfortunately, Exonerate or some such tool is ruled out due to constraint #3 above.

How about AUGUSTUS-PPX's fastBlockSearch? See this AUGUSTUS-PPX link.

For some time now, I have had problems with running AUGUSTUS-PPX standalone installation - not as part of MAKER or some other pipeline / wrapper. So AUGUSTUS had been excluded from my list of options until now, but ...

If anyone with recent success with using fastBlockSearch, please respond whether you think fastBlockSearch should work for my needs, at least in theory.

If not, could you please guide me to more appropriate tool(s) for such analyses?

Thank you!

[GenoMax]

Can you not satisfy requirement #3 by post processing Exonerate results?

[Anand Rao]

But exonerate , AFAIK, cannot use a protein HMM as a query. Can it?!