Hmmpfam manual

Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are retained on all copies. The HMMER software package is a copyrighted work that may be freely distributed and modified under the terms of the GNU General Public License as published by the Free Software. hmmpfam reads a single sequence from seqfile and compares it against all the HMMs in hmmfile looking for significantly similar sequence matches. hmmfile will be looked for first in the current working directory, then in a directory named by the environment variable HMMERDB. Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearchMissing: manual.

hmmindex - create a binary GSI index for an HMM database. Synopsis hmmindex [options] database. Description. hmmindex is a utility that creates a binary GSI ("generic sequence index" format) index for an HMM database file called database. Pfam (November , entries) The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). hmmsearch reads an HMM from hmmfile and searches seqfile for significantly similar sequence matches. seqfile will be looked for first in the current working directory, then in a directory named by the environment variable BLASTDB. This lets users use existing BLAST databases, if BLAST has been configured for the site.

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