.TH "hmmer" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual".SH NAME.TP HMMER - profile hidden Markov model software.SH SYNOPSIS.TP.B hmmalignAlign multiple sequences to a profile HMM..TP.B hmmbuildBuild a profile HMM from a given multiple sequence alignment..TP.B hmmcalibrateDetermine appropriate statistical significance parameters for a profile HMM prior to doing database searches..TP .B hmmconvertConvert HMMER profile HMMs to other formats, such as GCG profiles..TP.B hmmemitGenerate sequences probabilistically from a profile HMM..TP.B hmmfetchRetrieve an HMM from an HMM database.TP .B hmmindexCreate a binary SSI index for an HMM database.TP.B hmmpfamSearch a profile HMM database with a sequence (i.e., annotate variouskinds of domains in the query sequence)..TP.B hmmsearchSearch a sequence database with a profile HMM (i.e., find additionalhomologues of a modeled family). .SH DESCRIPTIONThese programs use profile hidden Markov models (profile HMMs) tomodel the primary structure consensus of a family of protein ornucleic acid sequences. .SH OPTIONS.PPAll.B HMMER programs give a brief summary of their command-line syntax and optionsif invoked without any arguments.When invoked with the single argument,.B -h(i.e., help), a program will report more verbose command-line usageinformation, including rarely used, experimental, and expert options..B -hwill report version numbers which are useful ifyou need to report a bug or problem to me..PPEach.B HMMERprogram has its own man page briefly summarizing command line usage.There is also a user's guide that camewith the software distribution, which includes a tutorial introductionand more detailed descriptions of the programs.See http://hmmer.wustl.edu/ for on-line documentation andthe current HMMER release..PPIn 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 usedand 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 importantin 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 experimentswith HMMER, and may not be supported or documented adequately. .SH SEQUENCE FILE FORMATSIn general,.B HMMERattempts to read most common biological sequence file formats.It autodetects the format of the file. It also autodetectswhether the sequences are protein or nucleic acid. Standard IUPAC degeneracy codes are allowed in additionto the usual 4-letter or 20-letter codes. .TP.B Unaligned sequencesUnaligned sequence files may be in FASTA, Swissprot, EMBL, GenBank,PIR, Intelligenetics, Strider, or GCG format. These formatsare documented in the User's Guide..TP .B Sequence alignmentsMultiple sequence alignments may be in CLUSTALW, SELEX, or GCG MSFformat. These formatsare documented in the User's Guide..SH ENVIRONMENT VARIABLESFor ease of using large stable sequence and HMM databases,.B HMMERlooks for sequence files and HMM files in the currentworking directory as well as in system directories specifiedby environment variables..TP.B BLASTDBSpecifies the directory location of sequence databases. Example:.B /seqlibs/blast-db/.In installations that use BLAST software, this environment variableis likely to already be set..TP.B HMMERDBSpecifies the directory location of HMM databases. Example:.B /seqlibs/pfam/.