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
acceleration 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