Hmmpgmd is a daemon for searching a protein query against a protein database. To use hmmpgmd, first an instance must be started up as a master server, and provided with at least one of a sequence database (using the --seqdb flag) and or or an HMM database (using the --hmmdb flag). A sequence database must be in the hmmpgmd format, which may be produced using esl-reformat. An HMM database is of the form produced by hmmbuild. The input database(s) will be loaded into memory by the master. When the master has finished loading the database(s), it prints
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.