https://wikimd.org/index.php?action=history&feed=atom&title=HMMERHMMER - Revision history2026-04-27T05:32:52ZRevision history for this page on the wikiMediaWiki 1.44.2https://wikimd.org/index.php?title=HMMER&diff=6347086&oldid=prevPrab: CSV import2025-02-25T20:51:27Z<p>CSV import</p>
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<p><b>New page</b></p><div>'''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. <br />
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== Overview ==<br />
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HMMER is designed to detect remote [[Protein homology|homologs]] as sensitively as possible, and to achieve high [[Statistical significance|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.<br />
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== Features ==<br />
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HMMER includes a number of features that make it a powerful tool for sequence analysis. These include:<br />
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* '''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.<br />
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* '''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.<br />
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* '''Ease of use''': HMMER is designed to be easy to use, with a simple command-line interface and comprehensive documentation.<br />
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== Applications ==<br />
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HMMER is used in a wide range of biological research applications, including:<br />
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* '''Protein domain identification''': HMMER can be used to identify protein domains in sequence data.<br />
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* '''Sequence alignment''': HMMER can be used to align sequences to profile HMMs, providing a powerful tool for sequence comparison and phylogenetic analysis.<br />
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* '''Database search''': HMMER can be used to search sequence databases for homologs of a given sequence or profile.<br />
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== See also ==<br />
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* [[Bioinformatics]]<br />
* [[Computational biology]]<br />
* [[Sequence alignment]]<br />
* [[Protein structure prediction]]<br />
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== References ==<br />
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<references /><br />
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== External links ==<br />
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* [http://hmmer.org/ Official HMMER website]<br />
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[[Category:Bioinformatics software]]<br />
[[Category:Free software]]<br />
[[Category:Computational biology]]<br />
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