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 "profile
hidden Markov models" (profile HMMs) to represent the likely evolutionary
homologs of a single sequence or a multiple alignment of a sequence family. A
main avenue of research is to improve the evolutionary 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 exponentially 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 multiple 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 alignment(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
programs 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 manageably
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 individual 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