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HMMER

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, and to perform sequence alignments. It detects homology by comparing a profile-HMM (a Hidden Markov model constructed explicitly for a particular search) to either a single sequence or…

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The HMMER web server

Web serverUniProtSwissProtProtein Data BankTIGRFAMs
10 related topics

Overview

FreeSean EddyHomologousProteinNucleotide
18 related topics

The HMMER3 release

Heuristic filterLog-likelihoodE-valuesForward scores
4 related topics

Programs in the HMMER package

DNARNAHMM logo
3 related topics

Key facts & relationships

High-confidence facts extracted from structured source data. Use them as anchors for further research.

Available in
English
Developers
Sean Eddy, Travis Wheeler, HMMER development team
License
BSD-3
Repository
github.com/EddyRivasLab/hmmer
Stable release
3.4 / 15 August 2023; 3 years ago (15 August 2023)
Type
Bioinformatics tool

Topics to explore

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Overview

Profile HMMs

Programs in the HMMER package

The HMMER web server

The HMMER3 release

Advanced semantic analysis

Deeper signals for content research, entity SEO and topical coverage. The plain-language headings explain what each technical view is useful for.

Map overview Semantic statistics

HMMER

Nodes43
Edges42
Triples65
Avg. degree1.95
Density0.046512
Components1

How this topic connects Entity context

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HMMER

Top relations

related to The HMMER web server · 12
HMMER → HMM, HMMs, In, Pfam, Programs, Protein Data Bank, Search, SUPERFAMILY, SwissProt, The, TIGRFAMs, UniProt
related to Improvements in speed · 10
HMMER → BLAST, BLAST-based, DNA-based, E-values, Further, HMM-based, HMMER3, The, This, While
related to The HMMER3 release · 5
HMMER → HMM, HMMER2, HMMER3, Major, The
related to Improvements in remote homology searching · 4
HMMER → HMMER3, In, The, While
related to DNA sequence comparison · 3
HMMER → DNA/DNA, HMMER2, HMMER3
related to External links · 3
HMMER → Archived, Official, Wayback Machine
related to Homology searching · 3
HMMER → DNA/RNA, HMM, HMMs
related to Programs in the HMMER package · 3
HMMER → Markov, The, The HMMER
related to Restriction to local alignments · 3
HMMER → HMMER3, This, While HMMER2
is a · 2
HMMER → console utility ported to every major operating system, free and commonly used software package for sequence analysis written by Sean Eddy

Important terminology Word statistics

Use these terms to understand the vocabulary surrounding the topic, not as a checklist for keyword stuffing.

Important terminology

sequence sequences alignment alignments profile hmmer3 states model package search used speed also protein homologous major profile-hmm hmms hmm searches

Entity relationships Subject–Predicate–Object triples

SubjectPredicateObjectConfidenceSrc
HMMERAvailable inEnglish1.00infobox
HMMERDevelopersSean Eddy, Travis Wheeler, HMMER development team1.00infobox
HMMERLicenseBSD-31.00infobox
HMMERRepositorygithub.com/EddyRivasLab/hmmer1.00infobox
HMMERStable release3.4 / 15 August 2023; 3 years ago (15 August 2023)1.00infobox
HMMERTypeBioinformatics tool1.00infobox
HMMERWebsitehmmer.org1.00infobox
HMMERWritten inC1.00infobox
HMMERis afree and commonly used software package for sequence analysis written by Sean Eddy0.90text
HMMERis aconsole utility ported to every major operating system0.90text
Pfaminstance ofand macOS.HMMER is the core utility that protein family databases0.80text
InterPro are based uponinstance ofand macOS.HMMER is the core utility that protein family databases0.80text

Related concept clusters Concept neighborhoods

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    Connections between topic areas Semantic bridges

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