Ubuntu Manpage: hmm2pfam - search one or more sequences against an HMM database

NAME

       hmm2pfam - search one or more sequences against an HMM database

SYNOPSIS

       hmm2pfam [options] hmmfile seqfile

DESCRIPTION

       hmm2pfam  reads  a sequence file seqfile and compares each sequence in it, one at a time, against all the
       HMMs in hmmfile looking for significantly similar sequence matches.

       hmmfile will be looked for first in the current working directory, then  in  a  directory  named  by  the
       environment  variable  HMMERDB.  This lets administrators install HMM library(s) such as Pfam in a common
       location.

       There is a separate output report for each sequence in seqfile.  This report consists of three  sections:
       a  ranked  list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence
       in the sequence, and alignments for all the best scoring domains.  A sequence score may be higher than  a
       domain  score  for the same sequence if there is more than one domain in the sequence; the sequence score
       takes into account all the domains.  All sequences scoring above the -E and -T cutoffs are shown  in  the
       first list, then every domain found in this list is shown in the second list of domain hits.  If desired,
       E-value and bit score thresholds may also be applied to the domain  list  using  the  --domE  and  --domT
       options.

OPTIONS

       -h     Print brief help; includes version number and summary of all options, including expert options.

       -n     Specify  that  models and sequence are nucleic acid, not protein.  Other HMMER programs autodetect
              this; but because of the order in which hmm2pfam accesses data, it can't  reliably  determine  the
              correct "alphabet" by itself.

       -A <n> Limits  the  alignment output to the <n> best scoring domains.  -A0 shuts off the alignment output
              and can be used to reduce the size of output files.

       -E <x> Set the E-value cutoff for the per-sequence ranked hit list to <x>, where <x> is a  positive  real
              number.  The  default  is  10.0. Hits with E-values better than (less than) this threshold will be
              shown.

       -T <x> Set the bit score cutoff for the per-sequence ranked hit list to <x>, where <x> is a real  number.
              The  default  is  negative infinity; by default, the threshold is controlled by E-value and not by
              bit score.  Hits with bit scores better than (greater than) this threshold will be shown.

       -Z <n> Calculate the E-value scores as if we had seen a sequence database of <n> sequences.  The  default
              is arbitrarily set to 59021, the size of Swissprot 34.

EXPERT OPTIONS

--acc Report HMM accessions instead of names in the output reports. Useful for high-throughput
annotation, where the data are being parsed for storage in a relational database.

--compat
Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers
don't have to be rewritten.

--cpu <n>
Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in
the machine. Overrides the HMMER_NCPU environment variable. Only affects threaded versions of
HMMER (the default on most systems).

--cut_ga
Use Pfam GA (gathering threshold) score cutoffs. Equivalent to --globT <GA1> --domT <GA2>, but
the GA1 and GA2 cutoffs are read from each HMM in hmmfile individually. hmm2build puts these
cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended
SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are
not set in the HMM file, --cut_ga doesn't work.

--cut_tc
Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to --globT <TC1> --domT <TC2>, but the TC1
and TC2 cutoffs are read from each HMM in hmmfile individually. hmm2build puts these cutoffs there
if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or
Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in
the HMM file, --cut_tc doesn't work.

--cut_nc
Use Pfam NC (noise cutoff) score cutoffs. Equivalent to --globT <NC1> --domT <NC2>, but the NC1
and NC2 cutoffs are read from each HMM in hmmfile individually. hmm2build puts these cutoffs there
if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or
Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in
the HMM file, --cut_nc doesn't work.

--domE <x>
Set the E-value cutoff for the per-domain ranked hit list to <x>, where <x> is a positive real
number. The default is infinity; by default, all domains in the sequences that passed the first
threshold will be reported in the second list, so that the number of domains reported in the per-
sequence list is consistent with the number that appear in the per-domain list.

--domT <x>
Set the bit score cutoff for the per-domain ranked hit list to <x>, where <x> is a real number.
The default is negative infinity; by default, all domains in the sequences that passed the first
threshold will be reported in the second list, so that the number of domains reported in the per-
sequence list is consistent with the number that appear in the per-domain list. Important note:
only one domain in a sequence is absolutely controlled by this parameter, or by --domT. The
second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of
the details of how HMMER works. HMMER requires at least one pass through the main model per
sequence; to do more than one pass (more than one domain) the multidomain alignment must have a
better score than the single domain alignment, and hence the extra domains must contribute
positive score. See the Users' Guide for more detail.

--forward
Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores.
Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is
a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER
have not confirmed this, however.

--informat <s>
Assert that the input seqfile is in format <s>; do not run Babelfish format autodection. This
increases the reliability of the program somewhat, because the Babelfish can make mistakes;
particularly recommended for unattended, high-throughput runs of HMMER. Valid format strings
include FASTA, GENBANK, EMBL, GCG, PIR, STOCKHOLM, SELEX, MSF, CLUSTAL, and PHYLIP. See the User's
Guide for a complete list.

--null2
Turn off the post hoc second null model. By default, each alignment is rescored by a
postprocessing step that takes into account possible biased composition in either the HMM or the
target sequence. This is almost essential in database searches, especially with local alignment
models. There is a very small chance that this postprocessing might remove real matches, and in
these cases --null2 may improve sensitivity at the expense of reducing specificity by letting
biased composition hits through.

--pvm Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program
hmm2pfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated
GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is
produced by the program hmm2index.) Because the PVM implementation is I/O bound, it is highly
recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy.
Optional PVM support must have been compiled into HMMER for --pvm to function.

--xnu Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In
trial experiments, --xnu appears to perform less well than the default post hoc null2 model.

COPYRIGHT

       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
       Freely distributed under the GNU General Public License (GPL).
       See the file COPYING in your distribution for details on redistribution conditions.

AUTHOR

       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA
       http://www.genetics.wustl.edu/eddy/