Expanding gene family using hmmer

Question

[el97004]

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!

Answer 1

[Mensur Dlakic]

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).

[el97004]

Thank you! aligned fasta format does indeed work.