hmmfetch(1) [debian man page]
hmmfetch(1) HMMER Manual hmmfetch(1) NAME
hmmfetch - retrieve profile HMM(s) from a file SYNOPSIS
hmmfetch [options] <hmmfile> <key> (retrieves HMM named <key>) hmmfetch -f [options] <hmmfile> <keyfile> (retrieves all HMMs listed in <keyfile>) hmmfetch --index [options] <hmmfile> (indexes <hmmfile> for fetching) DESCRIPTION
Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam database, for example). The <hmmfile> must be indexed first, using hmmfetch --index. The index is a binary file named <hmmfile>.ssi. The default mode is to retrieve a single profile by name or accession, called the <key>. For example: % hmmfetch Pfam-A.hmm Caudal_act % hmmfetch Pfam-A.hmm PF00045 With the -f option, a <keyfile> containing a list of one or more keys is read instead. The first whitespace-delimited field on each non- blank non-comment line of the <keyfile> is used as a <key>, and any remaining data on the line is ignored; this allows a variety of white- space delimited datafiles to be used as <keyfile>s. The <keyfile> argument can be a '-' (dash) character, in which case the keyfile is read from standard input; this allows unix ninjas to construct sophisticated invocations using pipes. By default, the HMM is printed to standard output in HMMER3 format. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. -f The second commandline argument is a <keyfile> instead of a single <key>. The first field on each line of the <keyfile> is used as a retrieval <key> (an HMM name or accession). Blank lines and comment lines (that start with a # character) are ignored. -o <f> Output HMM(s) to file <f> instead of to standard output. -O Output HMM(s) to individual file(s) named <key> instead of standard output. With the -f option, this can result in many files being created. --index Instead of retrieving one or more profiles from <hmmfile>, index the <hmmfile> for future retrievals. This creates a <hmmfile>.ssi binary index file. SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ @HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmfetch(1)
Check Out this Related Man Page
hmmstat(1) HMMER Manual hmmstat(1) NAME
hmmstat - display summary statistics for a profile file SYNOPSIS
hmmstat [options] <hmmfile> DESCRIPTION
The hmmstat utility prints out a tabular file of summary statistics for each profile in <hmmfile>. The columns are: idx The index of this profile, numbering each on in the file starting from 1. name The name of the profile. accession The optional accession of the profile, or "-" if there is none. nseq The number of sequences that the profile was estimated from. eff_nseq The effective number of sequences that the profile was estimated from, after HMMER applied an effective sequence number calculation such as the default entropy weighting. M The length of the model in consensus residues (match states). relent Mean relative entropy per match state, in bits. This is the expected (mean) score per consensus position. This is what the default entropy-weighting method for effective sequence number estimation focuses on, so for default HMMER3 models, you expect this value to reflect the default target for entropy-weighting. info Mean information content per match state, in bits. Probably not useful. Information content is a slightly different calculation than relative entropy. p relE Mean positional relative entropy, in bits. This is a fancier version of the per-match-state relative entropy, taking into account the transition (insertion/deletion) probabilities; it may be a more accurate estimation of the average score contributed per model consensus position. compKL Kullback-Leibler distance between the model's overall average residue composition and the default background frequency distribution. The higher this number, the more biased the residue composition of the profile is. Highly biased profiles can slow the HMMER3 accel- eration pipeline, by causing too many nonhomologous sequences to pass the filters. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ p@HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmstat(1)