HMMER(1) HMMER Manual HMMER(1)NAME
HMMER - profile HMMs for biological sequence analysis
SYNOPSIS
hmmalign
Align sequences to a profile
hmmbuild
Construct profile(s) from multiple sequence alignment(s)
hmmconvert
Convert profile file to various HMMER and non-HMMER formats
hmmemit
Sample sequences from a profile
hmmfetch
Retrieve profile HMM(s) from a file
hmmpress
Prepare an HMM database for hmmscan
hmmscan
Search sequence(s) against a profile database
hmmsearch
Search profile(s) against a sequence database
hmmsim
Collect profile score distributions on random sequences
hmmstat
Summary statistics for a profile file
jackhmmer
Iterative search of a protein sequence against a protein sequence
database
phmmer
Search a protein sequence against a protein sequence database
DESCRIPTION
HMMER is a suite of several programs for biological sequence alignment
and database homology search. It uses probabilistic models called "pro‐
file hidden Markov models" (profile HMMs) to represent the likely evo‐
lutionary homologs of a single sequence or a multiple alignment of a
sequence family. A main avenue of research is to improve the evolution‐
ary predictive models in HMMER to be able to recognize and accurately
align increasingly remote homologs, distant in time.
HMMER is also used as an organizational tool, to group the exponen‐
tially growing number of biological sequences into a vastly smaller set
of well-annotated sequence families. New sequences can be annotated by
comparison against curated sequence family databases of prebuilt HMMER
profiles, in addition or instead of comparison to the entire sequence
database. Databases such as Pfam, SMART, and TIGRfams, among others,
are based on this principle.
HMMER is used in three main modes: to search a sequence database for
new homologs of a sequence or a sequence family; to search a profile
database (like Pfam) to find what known family a query sequence belongs
to, or what domains it has; and to automatically construct large multi‐
ple alignments (i.e. with an effectively unlimited number of sequences)
using a profile representative of a sequence family.
Suppose you have a multiple sequence alignment of a sequence family of
interest, and you want to search a sequence database for additional
homologs. The hmmbuild program builds profile(s) from multiple align‐
ment(s). The hmmsearch program searches profile(s) against a sequence
database.
Suppose you have a single sequence of interest, and you want to search
a sequence database for additional homologs. The phmmer program
searches a single protein sequence against a protein sequence database.
The jackhmmer program does the same thing but iteratively -- homologs
detected in a previous round are incorporated into a new profile, and
the new profile is searched again. phmmer is used like BLASTP, and
jackhmmer is used like a protein PSI-BLAST. Currently these two pro‐
grams support only protein/protein comparison, but this will change
with time.
Suppose you have sequence(s) that you want to analyze using a HMMER-
based profile HMM database like Pfam (http://pfam.sanger.ac.uk). The
hmmpress program formats a profile HMM flatfile (such as the file you
would download from Pfam) into a HMMER binary database. The hmmscan
program searches sequence(s) against that database.
Suppose you want to align lots of sequences. You can construct a man‐
ageably small alignment of a representative set of sequences, build a
profile with hmmbuild, and use the hmmalign program to align any number
of sequences to that profile.
HMMER also includes some auxiliary tools for working with large profile
databases. hmmfetch fetches one or more profiles from a database.
hmmstat prints summary statistics about a profile file.
For compatibility with other profile software and previous versions of
HMMER, the hmmconvert program converts profiles to a few other formats.
We intend to add more support for other formats over time.
The hmmemit program generates (simulates) "homologous" sequences by
sampling from a profile. It can also generate a "consensus" sequence.
The hmmsim program is a simulator used for collecting statistics about
score distributions on random sequences.
Each program has its own man page.
SEE ALSO
This is a summary man page for the entire HMMER3 package. See individ‐
ual man pages [hmmbuild(1), for example] for usage, options, and
description of each program in the 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@ HMMER(1)
