HMMER - profile HMMs for biological sequence analysis
Align sequences to a profile
Construct profiles from multiple sequence alignments
Convert profile file to various formats
Sample sequences from a profile
Retrieve profiles from a file
Produce a conservation logo graphic from a profile
Daemon for database search web services
Prepare a profile database for hmmscan
Search sequence(s) against a profile database
Search profile(s) against a sequence database
Collect profile score distributions on random sequences
Summary statistics for a profile file
Iteratively search sequence(s) against a sequence database
build nhmmer database from a sequence file
Search DNA/RNA queries against a DNA/RNA sequence database
Search DNA/RNA sequence(s) against a DNA/RNA profile database
Search protein sequence(s) against a protein sequence database
Calculate and add column mask to a multiple sequence alignment
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
program builds profile(s) from multiple alignment(s). The
program searches protein profile(s) against a protein
sequence database, and nhmmer
searches nucleotide profile(s) against a
nucleotide sequence database.
Suppose you have a single sequence of interest, and you want to search a
sequence database for additional homologs. The phmmer
a single protein sequence against a protein sequence database. The
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
is used like a protein PSI-BLAST. The nhmmer
searches a single nucleotide sequence against a nucleotide sequence.
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
protein sequence(s) against that database. The nhmmscan
similarly search nucleotide sequence(s) against a pressed database of
nucleotide profiles, such as from Dfam (http://dfam.janelia.org).
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
, 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
fetches one or more profiles from a database.
prints summary statistics about a profile file.
For compatibility with other profile software and previous versions of HMMER,
program converts profiles to a few other formats. We
intend to add more support for other formats over time.
program generates (simulates) "homologous"
sequences by sampling from a profile. It can also generate a
program is a simulator used for collecting statistics about
score distributions on random sequences.
Each program has its own man page.
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 (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