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hmmemit

By Finn R., Eddy S., Last update 1494698999
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hmmemit description

Hmmemit samples (emits) sequences from the profile HMM(s) in hmmfile, and writes them to output. Sampling sequences may be useful for a variety of purposes, including creating synthetic true positives for benchmarks or tests. The hmmemit program samples (emits) sequences from the profile HMM(s) in hmmfile, and writes them to output. Sampling sequences may be useful for a variety of purposes, including creating synthetic true positives for benchmarks or tests. As another option, with the -p option you can sample a sequence from a fully configured HMMER search profile. This means sampling a *homologous sequence* by HMMER*s definition, including nonhomologous flanking sequences, local alignments, and multiple domains per sequence, depending on the length model and alignment mode chosen for the profile.


Parent program: hmmer

HMMER software allows search for protein homologs and also permits multiple protein sequence alignment. Unlike BLAST, HMMER uses probabilistic models called profile hidden Markov models which provide a significantly more accurate and more sensitive detection of remote homologs. The HMMER software suite has been widely used, particularly for protein family databases such as Pfam and InterPro and their associated search tools. Also HMMER has several programs for protein sequence analysis such as phmmer, hmmscan, hmmsearch and jackhmmer.