     hmmer(1)                        HMMER 2.1.1                        hmmer(1)
     HMMER Manual                                                   HMMER Manual

                                      Dec 1998

     NAME
          HMMER - profile hidden Markov model software

     SYNOPSIS
          hmmalign
               Align multiple sequences to a profile HMM.

          hmmbuild
               Build a profile HMM from a given multiple sequence alignment.

          hmmcalibrate
               Determine appropriate statistical significance parameters for a
               profile HMM prior to doing database searches.

          hmmconvert
               Convert HMMER profile HMMs to other formats, such as GCG profiles.

          hmmemit
               Generate sequences probabilistically from a profile HMM.

          hmmpfam
               Search a profile HMM database with a sequence (i.e., annotate
               various kinds of domains in the query sequence).

          hmmsearch
               Search a sequence database with a profile HMM (i.e., find
               additional homologues of a modeled family).

     DESCRIPTION
          These programs use profile hidden Markov models (profile HMMs) to
          model the primary structure consensus of a family of protein or
          nucleic acid sequences.

     OPTIONS
          All HMMER programs give a brief summary of their command-line syntax
          and options if invoked without any arguments.  When invoked with the
          single argument, -h (i.e., help), a program will report more verbose
          command-line usage information, including rarely used, experimental,
          and expert options.  -h will report version numbers which are useful
          if you need to report a bug or problem to me.

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     hmmer(1)                        HMMER 2.1.1                        hmmer(1)
     HMMER Manual                                                   HMMER Manual

                                      Dec 1998

          Each HMMER program has its own man page briefly summarizing command
          line usage.  There is also a user's guide that came with the software
          distribution, which includes a tutorial introduction and more detailed
          descriptions of the programs.

          See http://hmmer.wustl.edu/ for on-line documentation and the current
          HMMER release.

          In general, no command line options should be needed by beginning
          users.  The defaults are set up for optimum performance in most
          situations.  Options that are single lowercase letters (e.g. -a ) are
          "common" options that are expected to be frequently used and will be
          important in many applications.  Options that are single uppercase
          letters (e.g. -B ) are usually less common options, but also may be
          important in some applications.  Options that are full words (e.g. --
          verbose ) are either rarely used, experimental, or expert options.
          Some experimental options are only there for my own ongoing
          experiments with HMMER, and may not be supported or documented
          adequately.

     SEQUENCE FILE FORMATS
          In general, HMMER attempts to read most common biological sequence
          file formats.  It autodetects the format of the file. It also
          autodetects whether the sequences are protein or nucleic acid.
          Standard IUPAC degeneracy codes are allowed in addition to the usual
          4-letter or 20-letter codes.

          Unaligned sequences
               Unaligned sequence files may be in FASTA, Swissprot, EMBL,
               GenBank, PIR, Intelligenetics, Strider, or GCG format. These
               formats are documented in the User's Guide.

          Sequence alignments
               Multiple sequence alignments may be in CLUSTALW, SELEX, or GCG
               MSF format. These formats are documented in the User's Guide.

     ENVIRONMENT VARIABLES
          For ease of using large stable sequence and HMM databases, HMMER looks
          for sequence files and HMM files in the current working directory as
          well as in system directories specified by environment variables.

          BLASTDB

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     hmmer(1)                        HMMER 2.1.1                        hmmer(1)
     HMMER Manual                                                   HMMER Manual

                                      Dec 1998

               Specifies the directory location of sequence databases. Example:
               /seqlibs/blast-db/. In installations that use BLAST software,
               this environment variable is likely to already be set.

          HMMERDB
               Specifies the directory location of HMM databases. Example:
               /seqlibs/pfam/.

     SEE ALSO
          hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex
          hmmpfam hmmsearch

          User guide and tutorial: Userguide.ps

          WWW: http://hmmer.wustl.edu/

     AUTHOR
          This software and documentation is Copyright (C) 1992-1998 Washington
          University School of Medicine.  It is freely distributable under terms
          of the GNU General Public License. See COPYING in the source code
          distribution for more details, or contact me.

          Sean Eddy
          Dept. of Genetics
          Washington Univ. School of Medicine
          4566 Scott Ave.
          St Louis, MO 63110 USA
          Phone: 1-314-362-7666
          FAX  : 1-314-362-7855
          Email: eddy@genetics.wustl.edu

                                        - 3 -       Formatted:  December 8, 1999