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HMMER: Art & Products

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…

Language: English [EN]
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HMMER topic overview

The analysis highlights Art and Products as prominent areas in the source structure around HMMER.

Related topics
36
Source areas
5
Connected nodes
42
Extracted relationships
65
Concept neighborhoods
20
Bridge connections
42

What this topic covers Research coverage

Source areas are shown by the number of related topics found in each part of the analysis. Use smaller areas too: they can reveal specialized angles and content gaps.

Overview · 18 topics
The HMMER web server · 9 topics
The HMMER3 release · 4 topics
Programs in the HMMER package · 3 topics
Profile HMMs · 2 topics

Smaller areas are not necessarily less important. They contain fewer connections in this analysis and can be useful for finding specialized angles or coverage gaps.

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

Explore all related topics Closing gaps

Browse the complete topic structure, not only the most central items. Less prominent entities and concepts can reveal missing angles, specialized context and useful research gaps. Each item opens a new analysis centered on that subject.

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.

How HMMER connects Entity context

The extracted context around HMMER shows recurring relationship patterns in the source. For example, HMMER → HMM, HMMs, In, Pfam, Programs, Protein Data Bank, Search, SUPERFAMILY, SwissProt, The, TIGRFAMs, UniProt Another extracted example is HMMER → BLAST, BLAST-based, DNA-based, E-values, Further, HMM-based, HMMER3, The, This, While. Use these groups to spot repeated connection types before inspecting the individual relationships.

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

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

HMMER relationships Subject–Predicate–Object triples

TTTA extracted 65 structured relationships around HMMER. Examples in this analysis include HMMER → Available in → English and HMMER → Developers → Sean Eddy, Travis Wheeler, HMMER development team. The table shows each extracted connection, where it came from and its confidence.

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

The concept neighborhoods around HMMER bring nearby vocabulary together. In this analysis, examples include Package, Software and Web. Use the clusters to find adjacent concepts and terminology that may deserve separate research.

  • HMMER
    • Package
    • Software
    • Web
    • Also
    • Major
    • Searches
    • Speed
    • Hmmer3
    • Release
    • Based
    • Bioinformatics
    • Sean
  • hmmer
    • Package
    • Software
    • Web
    • Also
    • Major
    • Searches
    • Speed
    • Hmmer3
    • Release
    • Based
    • Bioinformatics
    • Sean
  • multiple sequence alignment
    • Alignment
    • Sequence
    • Alignments
    • Profile
    • Sequences
    • Hmm
    • Hmms
    • Model
    • States
    • Multiple
    • Package
    • Search
  • hmm logo
    • Dna
    • Pfam
    • Profile
    • Programs
    • Protein
    • Sequence
    • Hmms
    • Package
    • Release
    • Homology
    • Markov
    • Nucleotide
  • profile hmms
    • Profile
    • Hmm
    • Sequences
    • Dna
    • Sequence
    • Search
    • Programs
    • Multiple
    • Used
    • Package
    • States
    • Release
  • programs in the hmmer package
    • Programs
    • Package
    • Dna
    • Sean
    • Software
    • Web
    • Hmm
    • Multiple
    • Profile
    • Release
    • Search
    • Using
  • the hmmer web server
    • Bioinformatics
    • Sean
    • Package
    • Also
    • Release
    • Hmmer
    • Software
    • Web
    • Dna
    • Homology
    • Major
    • Searches
  • hidden markov model
    • Markov
    • Used
    • Model
    • Hmmer2
    • Profile-hmm
    • Sequence
    • Homology
    • Particular
    • Pfam
    • Sequences
    • Profile
    • Programs

Connections between topic areas Semantic bridges

For HMMER, one of the stronger structural bridges in this analysis connects HMMER with Overview. Bridges highlight paths between different parts of the map and can reveal research angles that are easy to miss in a flat list.

Min side: 3
HMMER — Overview · splits 24 ⟂ 19
HMMER — The HMMER web server · splits 32 ⟂ 11
HMMER — The HMMER3 release · splits 38 ⟂ 5
HMMER — Programs in the HMMER package · splits 39 ⟂ 4
HMMER — Profile HMMs · splits 40 ⟂ 3

Map overview Semantic statistics

HMMER

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

Source & methodology

TTTA analyzes the structure around HMMER to surface related topics, entities, relationships, concept neighborhoods and bridge connections. Use the map to explore areas such as Art & Products, including less central topics that may reveal useful research gaps. Automatically extracted connections are research leads rather than rewritten encyclopedia content.

Source: Wikipedia — HMMER · EN edition · Analysis: TopicsToTalkAbout

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