hmmstat - summary statistics for a profile file
utility prints out a tabular file of summary statistics for
each profile in hmmfile
may be '-' (a dash character), in which case profiles are read
from a stdin pipe instead of from a file.
The columns are:
- The index of this profile, numbering each on in the file starting from 1.
- The name of the profile.
- The optional accession of the profile, or "-" if there is none.
- The number of sequences that the profile was estimated from.
- 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.
- The length of the model in consensus residues (match states).
- 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.
- Mean information content per match state, in bits. Probably not useful.
Information content is a slightly different calculation than relative
- 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.
- 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.
- Help; print a brief reminder of command line usage and all available
(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 (http://hmmer.org/).
Copyright (C) 2018 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page