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Make a multiple sequence alignment with a HMMER hmmsearch output?

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.

hmmer
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updated by h.mon h.mon • written by westin.kosater • westin.kosater

1 answer

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

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written by h.mon h.mon

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