How to concatenate different domains in the target database identified by hmmsearch

Question

[Yongjie Zhang]

Dear all,

After performing hmmsearch, each target sequence may contain two or more domains that are identified by searching with a profile. I'd like to extract those domain regions for future phylogenetic analysis. Do you know how to realize that goal?

Acturally, I have used esl-reformat to convert the .sto file to a .fas file. And I found the two domains from one original sequence are displayed as two or more sequences in the converted .fas file. That is not convenient for my downstream analysis. Is there a way to extract and concatenate different domain regions? Or, is there a way to extract just the domain with the best bit score?

Thanks,

Yongjie

[GenoMax]

See the answer here as an option -->How do I get all sequences for one specific domain from Hmmer vs Pfam output that contains the results of many domains ?