hmmscan

hmmscan description

Hmmscan is used to search protein sequences against collections of protein profiles. For each sequence in , use that query sequence to search the target database of profiles in , and output ranked lists of the profiles with the most significant matches to the sequence. The may contain more than one query sequence. It can be in FASTA format, or several other common sequence file formats (genbank, embl, and uniprot, among others), or in alignment file formats (stockholm, aligned fasta, and others). See the --qformat option for a complete list.

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.