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

Hmmsim collects score distributions on random sequences. The hmmsim program generates random sequences, scores them with the model(s) in , and outputs various sorts of histograms, plots, and fitted distributions for the resulting scores. hmmsim is not a mainstream part of the HMMER package. Most users would have no reason to use it. It is used to develop and test the statistical methods used to determine P-values and E-values in HMMER3. For example, it was used to generate most of the results in a 2008 paper on H3*s local alignment statistics (PLoS Comp Bio 4:e1000069, 2008; http: or or www.ploscompbiol.org or doi or pcbi.1000069).

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.