This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Expanding gene family using hmmer

Hi all,

I have a list of proteins that belong to an orthogroup, and id like to expand this gene family by searching for more members iteratively. I have read that jackhmmer in the HMMER package can do this however I am confused on the input. If i create an HMM profile and use that as input I get an error message:

Error: Sequence file ortho1.hmm is empty or misformatted

So I am thinking of just giving it the protein sequences (not in a HMM profile) however I would need to ensure that it can make a profile with those sequences and use that to search iteratively, and output the final hmm model at the end. Anyone have experience with this and can give any advice?

Thank you!

hmmer jackhmmer sequence homology
• 1,573 views • link
updated by Mensur Dlakic Mensur Dlakic • written by el97004 • el97004

1 answer

It seems that you are feeding an HMM file to jackhmmer, which won't work. The error message tells you so. However, the alignment you used to build that HMM should be a valid input as long as it is in one of common formats (aligned FASTA, clustal, stockholm, etc).

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Thank you! aligned fasta format does indeed work.

• 0 views • link
written by el97004 • el97004

Log in to answer this question.

More posts like this