.TH "hmmer" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP HMMER - profile hidden Markov model software .SH SYNOPSIS .TP .B hmmalign Align multiple sequences to a profile HMM. .TP .B hmmbuild Build a profile HMM from a given multiple sequence alignment. .TP .B hmmcalibrate Determine appropriate statistical significance parameters for a profile HMM prior to doing database searches. .TP .B hmmconvert Convert HMMER profile HMMs to other formats, such as GCG profiles. .TP .B hmmemit Generate sequences probabilistically from a profile HMM. .TP .B hmmfetch Retrieve an HMM from an HMM database .TP .B hmmindex Create a binary SSI index for an HMM database .TP .B hmmpfam Search a profile HMM database with a sequence (i.e., annotate various kinds of domains in the query sequence). .TP .B hmmsearch Search a sequence database with a profile HMM (i.e., find additional homologues of a modeled family). .SH 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. .SH OPTIONS .PP All .B HMMER programs give a brief summary of their command-line syntax and options if invoked without any arguments. When invoked with the single argument, .B -h (i.e., help), a program will report more verbose command-line usage information, including rarely used, experimental, and expert options. .B -h will report version numbers which are useful if you need to report a bug or problem to me. .PP Each .B 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. .PP 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. .B -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 -B ) are usually less common options, but also may be important in some applications. Options that are full words (e.g. .B --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. .SH SEQUENCE FILE FORMATS In general, .B 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. .TP .B 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. .TP .B Sequence alignments Multiple sequence alignments may be in CLUSTALW, SELEX, or GCG MSF format. These formats are documented in the User's Guide. .SH ENVIRONMENT VARIABLES For ease of using large stable sequence and HMM databases, .B HMMER looks for sequence files and HMM files in the current working directory as well as in system directories specified by environment variables. .TP .B BLASTDB Specifies the directory location of sequence databases. Example: .B /seqlibs/blast-db/. In installations that use BLAST software, this environment variable is likely to already be set. .TP .B HMMERDB Specifies the directory location of HMM databases. Example: .B /seqlibs/pfam/.
