TIGRFAMs is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations.
The Genome Properties database specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. Content derives both from subsystem discovery work and from biocuration of the scientific literature.
To cite the TIGRFAMs resource, please reference "TIGRFAMs: a protein family resource for the functional identification of proteins."
Nucleic acids research. 2017-01-04; 45.D1: D190-D199.
InterPro in 2017-beyond protein family and domain annotations
PloS one. 2017-01-01; 12.6: e0171758.
A comprehensive software suite for protein family construction and functional site prediction
Nucleic acids research. 2015-01-01; 43.Database issue: D213-21.
The InterPro protein families database: the classification resource after 15 years
Nucleic acids research. 2013-01-01; 41.Database issue: D387-95.
TIGRFAMs and Genome Properties in 2013
Nucleic acids research. 2012-01-01; 40.Database issue: D306-12.
InterPro in 2011: new developments in the family and domain prediction database
Nucleic acids research. 2009-01-01; 37.Database issue: D211-5.
InterPro: the integrative protein signature database
Nucleic acids research. 2007-01-01; 35.Database issue: D224-8.
New developments in the InterPro database
Nucleic acids research. 2007-01-01; 35.Database issue: D260-4.
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Nucleic acids research. 2005-01-01; 33.Database issue: D201-5.
InterPro, progress and status in 2005
Nucleic acids research. 2003-01-01; 31.1: 371-3.
The TIGRFAMs database of protein families
Nucleic acids research. 2003-01-01; 31.1: 315-8.
The InterPro Database, 2003 brings increased coverage and new features
Briefings in bioinformatics. 2002-09-01; 3.3: 236-45.
HMM-based databases in InterPro
Nucleic acids research. 2001-01-01; 29.1: 41-3.
TIGRFAMs: a protein family resource for the functional identification of proteins
This project was funded through National Science Foundation (NSF), grant number 1458808.