Question: Make a multiple sequence alignment with a HMMER hmmsearch output?
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gravatar for westin.kosater
9 months ago by
westin.kosater10 wrote:

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 • 489 views
ADD COMMENTlink modified 9 months ago by h.mon28k • written 9 months ago by westin.kosater10
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gravatar for h.mon
9 months ago by
h.mon28k
Brazil
h.mon28k wrote:

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

ADD COMMENTlink written 9 months ago by h.mon28k
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