PAST PROJECT

TIGRFAMS

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."

Publications

Nucleic acids research. 2017-01-04; 45.D1: D190-D199.
InterPro in 2017-beyond protein family and domain annotations
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL
PMID: 27899635
PloS one. 2017-01-01; 12.6: e0171758.
A comprehensive software suite for protein family construction and functional site prediction
Haft DR, Haft DH
PMID: 28182651
Nucleic acids research. 2015-01-01; 43.Database issue: D213-21.
The InterPro protein families database: the classification resource after 15 years
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD
PMID: 25428371
Nucleic acids research. 2013-01-01; 41.Database issue: D387-95.
TIGRFAMs and Genome Properties in 2013
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E
PMID: 23197656
Nucleic acids research. 2012-01-01; 40.Database issue: D306-12.
InterPro in 2011: new developments in the family and domain prediction database
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY
PMID: 22096229
Nucleic acids research. 2009-01-01; 37.Database issue: D211-5.
InterPro: the integrative protein signature database
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C
PMID: 18940856
Nucleic acids research. 2007-01-01; 35.Database issue: D224-8.
New developments in the InterPro database
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C
PMID: 17202162
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
Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O
PMID: 17151080
Nucleic acids research. 2005-01-01; 33.Database issue: D201-5.
InterPro, progress and status in 2005
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH
PMID: 15608177
Nucleic acids research. 2003-01-01; 31.1: 371-3.
The TIGRFAMs database of protein families
Haft DH, Selengut JD, White O
PMID: 12520025
Nucleic acids research. 2003-01-01; 31.1: 315-8.
The InterPro Database, 2003 brings increased coverage and new features
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM
PMID: 12520011
Briefings in bioinformatics. 2002-09-01; 3.3: 236-45.
HMM-based databases in InterPro
Bateman A, Haft DH
PMID: 12230032
Nucleic acids research. 2001-01-01; 29.1: 41-3.
TIGRFAMs: a protein family resource for the functional identification of proteins
Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O
PMID: 11125044

Funding

This project was funded through National Science Foundation (NSF), grant number 1458808.

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