Align sequences to a profile
Construct profile(s) from multiple sequence alignment(s)
Convert profile file to various HMMER and non-HMMER formats
Sample sequences from a profile
Retrieve profile HMM(s) from a file
Prepare an HMM 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
Iterative search of a protein sequence against a protein sequence database
Search a protein sequence against a protein sequence database
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
hmmbuild program builds profile(s) from multiple alignment(s).
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
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).
hmmpress program formats a profile HMM flatfile (such as the file you
would download from Pfam) into a HMMER binary database.
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
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
hmmconvert program converts profiles to a few other formats. We intend to add
more support for other formats over time.
hmmemit program generates (simulates) "homologous" sequences by sampling from
a profile. It can also generate a "consensus" sequence.
hmmsim 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