HMMER - AbsoluteAstronomy.com

HMMER is a free

Free software

Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...

and commonly used software package for sequence analysis written by Sean Eddy

Sean Eddy

Sean R. Eddy is a scientist who leads a research group at the Howard Hughes Medical Institute Janelia Farm Research Campus in Virginia, with interests in bioinformatics, computational biology and biological sequence analysis...

. Its general usage is to identify homologous

Homology (biology)

Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

or nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

sequences. It does this by comparing a profile-HMM

Hidden Markov model

A hidden Markov model is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved states. An HMM can be considered as the simplest dynamic Bayesian network. The mathematics behind the HMM was developed by L. E...

to either a single sequence or a database of sequences. Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the profile-HMM. Profile-HMMs are constructed from a multiple sequence alignment

Multiple sequence alignment

A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...

in the HMMER package using the hmmbuild program. The profile-HMM implementation used in the HMMER software was based on the work of Krogh and colleagues. HMMER is a console utility ported to every major operating system

Operating system

An operating system is a set of programs that manage computer hardware resources and provide common services for application software. The operating system is the most important type of system software in a computer system...

, including different versions of Linux

Linux

Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Windows

Microsoft Windows

Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

, and Mac OS

Mac OS

Mac OS is a series of graphical user interface-based operating systems developed by Apple Inc. for their Macintosh line of computer systems. The Macintosh user experience is credited with popularizing the graphical user interface...

.

HMMER is the core utility that protein family databases such as Pfam

Pfam

Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...

and InterPro

InterPro

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them....

are based upon. Some other bioinformatics tools such as UGENE

UGENE

UGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces...

also use HMMER.

HMMER3 is complete rewrite of the earlier HMMER2 package, with the aim of improving the speed of profile-HMM searches. The main performance gain is due to a heuristic filter that finds high-scoring un-gapped matches within database sequences to a query profile. This heuristic results in a computation time comparable to BLAST

BLAST

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...

with little impact on accuracy. Further gains in performance are due to a log-likelihood

Likelihood-ratio test

In statistics, a likelihood ratio test is a statistical test used to compare the fit of two models, one of which is a special case of the other . The test is based on the likelihood ratio, which expresses how many times more likely the data are under one model than the other...

model that requires no calibration for estimating E-values

P-value

In statistical significance testing, the p-value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true. One often "rejects the null hypothesis" when the p-value is less than the significance level α ,...

, and allows the more accurate forward scores to be used for computing the significance of a homologous

Homology (biology)

sequence.

HMMER3 also makes extensive use of vector instructions

SIMD

Single instruction, multiple data , is a class of parallel computers in Flynn's taxonomy. It describes computers with multiple processing elements that perform the same operation on multiple data simultaneously...

for increasing computational speed. This work is based upon earlier publication showing a significant acceleration of the Smith-Waterman algorithm for aligning two sequences.

External links

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See also

External links