TIGRFAMs at NCBI

The original TIGRFAMs database was a research project of The Institute for Genomic Research (TIGR) and its successor, the J. Craig Venter Institute (JCVI). TIGRFAMs is a collection of manually curated protein families focusing primarily on prokaryotic sequences.It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene symbols, protein family names, descriptive text, cross-references to related models in TIGRFAMs and other databases, and pointers to literature.

The TIGRFAMs database was transferred in April 2018 to the National Center for Biotechnology Information (NCBI), which now holds the creative commons license to this data and is responsible for maintaining and distributing this intellectual property. The database is used in NCBI's Prokaryotic Genome Annotation Pipeline for GenBank and RefSeq sequence annotation, and curators continue to revise existing models. TIGRFAMs are searchable in Entrez, and are available for download as a part of a larger collection of HMMs. Other components of that collection are NCBIFAMs (models built from scratch by NCBI curators) and models derived from a curated collection of protein clusters (PRK).

Data availabilty

The up-to-date versions of all TIGRFAM models are available for download by FTP as a component of the current release of PGAP HMMs. They are recognizable by an accession number beginning with “TIGR”, or by the source designation “JCVI”.

TIGRFAM models, as part of the NCBI collection of Protein Family Models, can be searched in Entrez. Searches in this collection can be limited to TIGRFAMs by adding "TIGRFAM[Filter]" to the query. More search options are described here.

For archival purposes, JCVI Release 15.0 (4488 families, September 16 2014), the final version of TIGRFAMS before its move to from JCVI to NCBI, is hosted on the NCBI FTP site. Currently, GO terms on TIGRFAMs are available at NCBI only from that directory.

TIGRFAMs data are made available under a Creative Commons Attribution-ShareAlike 4.0 license. A brief summary and full text of the license are available at Creative Commons.

Citing TIGRFAMs

If describing use of a TIGRFAM model in a publication, please cite the most recent publication describing NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP).

To construct a URL to a TIGRFAM model, append the accession number to the prefix https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/, e.g. https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/TIGR04071.

References

Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028. PMID: 33270901

Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 2001 Jan 1;29(1):41-3. PMID: 11125044

Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003 Jan 1;31(1):371-3. PMID: 12520025

Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4. Epub 2006 Dec 6. PMID: 17151080

Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D387-95. doi: 10.1093/nar/gks1234. Epub 2012 Nov 28. PMID: 23197656