6 citations
1 runs


By Finn R., Eddy S., Last update 1494698999
All tools Run this tool

jackhmmer description

Jackhmmer iteratively searches each query sequence in against the target sequence(s) in . The first iteration is identical to a phmmer search. For the next iteration, a multiple alignment of the query together with all target sequences satisfying inclusion thresholds is assembled, a profile is constructed from this alignment (identical to using hmmbuild on the alignment), and profile search of the is done (identical to an hmmsearch with 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.