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PROGRAM:

NAME

HMMER - profile hidden Markov model software

SYNOPSIS

hmm2align
Align multiple sequences to a profile HMM.

hmm2build
Build a profile HMM from a given multiple sequence alignment.

hmm2calibrate
Determine appropriate statistical significance parameters for a profile HMM prior
to doing database searches.

hmm2convert
Convert HMMER profile HMMs to other formats, such as GCG profiles.

hmm2emit
Generate sequences probabilistically from a profile HMM.

hmm2fetch
Retrieve an HMM from an HMM database

hmm2index
Create a binary SSI index for an HMM database

hmm2pfam
Search a profile HMM database with a sequence (i.e., annotate various kinds of
domains in the query sequence).

hmm2search
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.

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.janelia.org/ 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
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/.

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