standards > model/format > DOI:10.25504/FAIRsharing.n3rt95
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ready 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.

How to cite this record HMMER Profile File Format; HMMER Profile File Format; DOI:; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 23 2022 12:41 p.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.

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Additional Information

TeSS training resources 

Similarity searching, multiple sequence alignment and protein families - undergraduate lab


    No tools defined


No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Data Release

Data Access


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


No metrics standards defined

Related Databases (3)
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.


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Grant Number(s)

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