HMMER

HMMER is a free and commonly used software suite for sequence analysis. Its primary use is for the detection of homologous protein or nucleotide sequences. HMMER uses Hidden Markov Models (HMMs) to represent the patterns of conservation in a group of related sequences.

Overview

HMMER is designed to detect remote homologs as sensitively as possible, and to achieve high statistical confidence in its results. The software is widely used in Genomics, Proteomics, and Bioinformatics in general, for the analysis and annotation of sequence databases.

Features

HMMER includes a number of features that make it a powerful tool for sequence analysis. These include:

• Profile hidden Markov models: HMMER uses profile HMMs, which are a type of statistical model that allows for the representation of a multiple sequence alignment in terms of a position-specific scoring system.

• Sensitivity and speed: HMMER is designed to be both sensitive and fast. It uses a variety of algorithmic and heuristic techniques to achieve these goals.

• Ease of use: HMMER is designed to be easy to use, with a simple command-line interface and comprehensive documentation.

Applications

HMMER is used in a wide range of biological research applications, including:

• Protein domain identification: HMMER can be used to identify protein domains in sequence data.

• Sequence alignment: HMMER can be used to align sequences to profile HMMs, providing a powerful tool for sequence comparison and phylogenetic analysis.

• Database search: HMMER can be used to search sequence databases for homologs of a given sequence or profile.

See also

• Bioinformatics
• Computational biology
• Sequence alignment
• Protein structure prediction

External links

• Official HMMER website

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  A profile HMM modelling a multiple sequence alignment

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  Hmmer core Profile HMM