Question: Output Full Lenghth Search Of Hmmer Output
0
gravatar for Pappu
6.9 years ago by
Pappu1.9k
Pappu1.9k wrote:

I am wondering if it is possible to output full length sequences of hmmsearch matches. Otherwise I have to extract the sequence ids and download the full length sequences from uniprot. "-A" option only outputs the alignment of the matching parts of sequences.

hmmer • 1.5k views
ADD COMMENTlink written 6.9 years ago by Pappu1.9k

Your question is not clear. Which sequences do you want? Are you interested in the sequences that you use to query the model file? You should already have those. Note that a HMMER search does not match any individual sequence. Rather, it matches a profile which is constructed from a multiple alignment of (typically) several sequences.

ADD REPLYlink written 6.8 years ago by David Westergaard1.4k

I want to output the full length sequences of the hits.

ADD REPLYlink written 6.8 years ago by Pappu1.9k

I think perhaps you should investigate exactly what a Hidden Markov Model is.

ADD REPLYlink written 6.8 years ago by David Westergaard1.4k
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