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

Hmmalign aligns sequences to a profile HMM. Make a multiple alignment of many sequences to a common profile HMM. Perform a multiple sequence alignment of all the sequences in by aligning them individually to the profile HMM in . The new alignment is output to stdout in Stockholm format. The sequences in are aligned in unihit local alignment mode. Therefore they should already be known to contain only a single domain (or a fragment of one). The optimal alignment may assign some residues as nonhomologous (N and C states), in which case these residues are still included in the resulting alignment, but shoved to the outer edges. To trim these unaligned nonhomologous residues from the result, see the --trim option.

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.