is there a tblastn-version of hmmsearch i.e. search protein profile against nucleotide database?
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4.1 years ago
wl284 ▴ 70

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 • 2.4k views
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4.1 years ago
Sej Modha 4.9k

HMMER might be useful for this.

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

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

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