Question: is there a tblastn-version of hmmsearch i.e. search protein profile against nucleotide database?
gravatar for wl284
3.7 years ago by
wl28460 wrote:

I'm trying to look for some mitochondrial genes that could be highly divergent in a genomic assembly using a hmm profile of translated genes from other organisms.

Normally I use hmmbuild to make a profile and hmmsearch (both from HMMER) to search a database of protein sequences but I was wondering whether there was any way of searching the nucleotide sequences directly using the hmm profile, without having to translate them first, similar to how you can search nucleotide databases with protein sequences using tblastn?

blast sequence • 2.2k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by wl28460
gravatar for Sej Modha
3.7 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

HMMER might be useful for this.

ADD COMMENTlink written 3.7 years ago by Sej Modha4.7k

Yes, I'm referring to the hmmsearch within the HMMER package. I'll update my question to be more specific.

ADD REPLYlink written 3.7 years ago by wl28460

Did you ever find a good solution for this? Thanks!

ADD REPLYlink written 2.1 years ago by dp40
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