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- HMMER abstract "HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences. It does this by comparing a profile-HMM 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 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, including different versions of Linux, Windows, and Mac OS.HMMER is the core utility that protein family databases such as Pfam and InterPro are based upon. Some other bioinformatics tools such as UGENE 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 with little impact on accuracy. Further gains in performance are due to a log-likelihood model that requires no calibration for estimating E-values, and allows the more accurate forward scores to be used for computing the significance of a homologous sequence.HMMER3 also makes extensive use of vector instructions for increasing computational speed. This work is based upon earlier publication showing a significant acceleration of the Smith-Waterman algorithm for aligning two sequences.".
- HMMER wikiPageExternalLink probe1.0.
- HMMER wikiPageExternalLink hmmer.janelia.org.
- HMMER wikiPageExternalLink hmmer.org.
- HMMER wikiPageExternalLink metameme.sdsc.edu.
- HMMER wikiPageExternalLink ?p=127.
- HMMER wikiPageExternalLink ?p=6.
- HMMER wikiPageExternalLink www.blocks.fhcrc.org.
- HMMER wikiPageExternalLink sam.html.
- HMMER wikiPageExternalLink Wise2.
- HMMER wikiPageExternalLink pftools.
- HMMER wikiPageExternalLink psi1.html.
- HMMER wikiPageExternalLink hmmer_on_tesla.html.
- HMMER wikiPageExternalLink decypherhmm.
- HMMER wikiPageID "19535600".
- HMMER wikiPageRevisionID "645700897".
- HMMER developer "Sean Eddy".
- HMMER genre "Bioinformatics tool".
- HMMER hasPhotoCollection HMMER.
- HMMER language English_language.
- HMMER latestPreviewVersion "3.1".
- HMMER latestReleaseVersion "3".
- HMMER license GNU_General_Public_License.
- HMMER name "HMMER".
- HMMER programmingLanguage C_(programming_language).
- HMMER subject Category:Bioinformatics.
- HMMER subject Category:Bioinformatics_software.
- HMMER subject Category:Computational_science.
- HMMER subject Category:Free_science_software.
- HMMER subject Category:Free_software_programmed_in_C.
- HMMER type Abstraction100002137.
- HMMER type Code106355894.
- HMMER type CodingSystem106353757.
- HMMER type Communication100033020.
- HMMER type Software106566077.
- HMMER type Writing106359877.
- HMMER type WrittenCommunication106349220.
- HMMER comment "HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences. It does this by comparing a profile-HMM 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.".
- HMMER label "HMMER".
- HMMER sameAs m.04n5g57.
- HMMER sameAs Q5631078.
- HMMER sameAs Q5631078.
- HMMER sameAs HMMER.
- HMMER wasDerivedFrom HMMER?oldid=645700897.
- HMMER homepage hmmer.org.
- HMMER isPrimaryTopicOf HMMER.