Make a multiple sequence alignment with a HMMER hmmsearch output?

Question

[westin.kosater]

I have a database of protein sequences and I just did a search (hmmsearch) through the database against my hmmfile using HMMER for all sequence with an E value cutoff. I saved my output from that to a text file, but now I want to do a multiple sequence alignment with the sequences from hmmsearch and fit a new HMM to these sequences. I have no idea how to do this, since I can't exactly do a MSA with the output from hmmsearch because it doesn't output the results to a recognized file format.

Answer 1

[h.mon]

See Creating multiple alignments with hmmalign (page 48) at the HMMER User’s Guide.