HMMER Profile File Format

General Information

The profile hidden Markov Model (HMM) calculated from multiple sequence alignment data in this service is stored in Profile HMM save format (usually with ".hmm" extension). It is an ASCII file containing a lot of header and descriptive records followed by large numerical matrix which holds a probabilistic model of the motif. The file of this format is useful to search against sequence databases to find other proteins which share the same motif.

Homepage http://www.hmmer.org

Countries that developed this resource European Union , United Kingdom , United States

Created in 1993

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Feb 22 2020 1:04 a.m.

Publication for citation HMMER web server: 2015 update. Finn RD,Clements J,Arndt W,Miller BL,Wheeler TJ,Schreiber F,Bateman A,Eddy SR; Nucleic Acids Res ; 2015; 10.1093/nar/gkv397;

Record updated: Jan. 17, 2019, 11:15 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.n3rt95' by 'The FAIRsharing Team' at 11:15, 17 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			Harvard University, Cambridge, MA, USA|http://www.harvard.edu|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		After:
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			Harvard University, Cambridge, MA, USA|http://www.harvard.edu|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Added:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Removed:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined

	'supportLinks' has been modified:
		Before:
			blog|https://cryptogenomicon.org/category/hmmer/
			online documentation|http://www.hmmer.org/publications.html
			online documentation|http://www.hmmer.org/documentation.html
			tess training|https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab
		After:
			TeSS training|https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab
			blog|https://cryptogenomicon.org/category/hmmer/
			online documentation|http://www.hmmer.org/publications.html
			online documentation|http://www.hmmer.org/documentation.html
		Added:
			TeSS training|https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab
		Removed:
			tess training|https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab

Edits to 'https://fairsharing.org/FAIRsharing.n3rt95' by 'The FAIRsharing Team' at 11:15, 17 Jan 2019 (approved):

	'supportLinks' has been modified:
		Before:
			online documentation|http://eddylab.org/publications/Eddy95b/Eddy95b-reprint.pdf
		After:
			blog|https://cryptogenomicon.org/category/hmmer/
			online documentation|http://www.hmmer.org/publications.html
			online documentation|http://www.hmmer.org/documentation.html
			tess training|https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab
		Added:
			blog|https://cryptogenomicon.org/category/hmmer/
			online documentation|http://www.hmmer.org/publications.html
			online documentation|http://www.hmmer.org/documentation.html
			tess training|https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab
		Removed:
			online documentation|http://eddylab.org/publications/Eddy95b/Eddy95b-reprint.pdf

	'miriam_id' has been modified:
		Before: None
		After: 

	'dataProcesses' has been modified:
		Before:
		After:
			HMMER Algorithm Releases
			HMMER Homology Search
		Added:
			HMMER Algorithm Releases
			HMMER Homology Search
		Removed:

	'organizations' has been modified:
		Before:
			Harvard University, Cambridge, MA, USA|http://www.harvard.edu|Maintains
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		After:
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			Harvard University, Cambridge, MA, USA|http://www.harvard.edu|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains

Edits to 'https://fairsharing.org/FAIRsharing.n3rt95' by 'The FAIRsharing Team' at 11:41, 14 Nov 2017 (approved):

	'domains' has been modified:
		Before:
			Amino acid sequence|material|http://edamontology.org/data_2976
			Genetic variation||http://edamontology.org/topic_0199
			Hidden Markov model (HMM)||http://edamontology.org/data_1364
			Life Science|domain|
			Multiple sequence alignment||http://edamontology.org/operation_0492
			Sequence motif||http://edamontology.org/data_1353
		After:
			Amino acid sequence|material|http://edamontology.org/data_2976
			Genetic variation||http://edamontology.org/topic_0199
			Hidden Markov model (HMM)||http://edamontology.org/data_1364
			Life Science|domain|
			Multiple sequence alignment||http://edamontology.org/operation_0492
			Sequence motif||http://edamontology.org/data_1353
			Homologous||http://purl.obolibrary.org/obo/SO_0000857
		Added:
			Homologous||http://purl.obolibrary.org/obo/SO_0000857
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.n3rt95' by 'The FAIRsharing Team' at 19:44, 26 Nov 2016 (approved):

	'homepage' has been modified:
		Before: http://www.genome.jp/tools/motif/hmmformat.htm
		After: http://www.hmmer.org

Edits to 'https://fairsharing.org/FAIRsharing.n3rt95' by 'The FAIRsharing Team' at 16:26, 20 Oct 2016 (approved):

	'name' has been modified:
		Before: HMMER Format
		After: HMMER Profile File Format

Support

General

blog	HMMER Blog
online documentation	Publications
online documentation	HMMER Documentation

Additional Information

Contact

Robert D Finn

TeSS training resources

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Data Release

HMMER Algorithm Releases

http://www.hmmer.org/download.html

Data Access

HMMER Homology Search

https://www.ebi.ac.uk/Tools/hmmer/

Publications

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.

Wistrand M,Sonnhammer EL
BMC Bioinformatics 2005

View Paper (PubMed) View Publication

HMMER web server: 2015 update.

Finn RD,Clements J,Arndt W,Miller BL,Wheeler TJ,Schreiber F,Bateman A,Eddy SR
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (3)

Pfam
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.

Type IV Secretion system Resource
A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.

3D interacting domains
The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

The Wellcome Trust, UK (Charitable foundation)
European Commission under FP7 Grant Agreement (Government body)

Maintains

Harvard University, Cambridge, MA, USA (University)
Howard Hughes Medical Institute (Research institute) Lead
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)

Grant Number(s)

108433/Z/15/Z (The Wellcome Trust, UK)

HMMER Profile File Format

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