Output Full Lenghth Search Of Hmmer Output
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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.
I want to output the full length sequences of the hits.
I think perhaps you should investigate exactly what a Hidden Markov Model is.