TIGRFAMs explained

TIGRFAMs is a database of protein families designed to support manual and automated genome annotation.^{[1] [2] [3]} Each entry includes a multiple sequence alignment and hidden Markov model (HMM) built from the alignment. Sequences that score above the defined cutoffs of a given TIGRFAMs HMM are assigned to that protein family and may be assigned the corresponding annotations. Most models describe protein families found in Bacteria and Archaea.

Like Pfam, TIGRFAMs uses the HMMER package written by Sean Eddy.^[4]

History

TIGRFAMs was produced originally at The Institute for Genomic Research (TIGR) and its successor, J. Craig Venter Institute (JCVI), but it moved in April 2018 to the National Center for Biotechnology Information (NCBI). TIGRFAMs remains a member database in InterPro. The last version from JCVI, release 15.0, contained 4488 models. TIGRFAMs now continues at NCBI as part of a larger collection of HMMs, called NCBIFAMs, used in its RefSeq and PGAP genome annotation pipelines.^[5] Active curation and revision of TIGRFAMs models continues at NCBI, but the creation of TIGRFAMs models per se has ended, as newly constructed HMMs from the RefSeq group receive different designations when added to NCBIFAMs.

External links

• https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/ - TIGRFAMs home page
• https://www.ebi.ac.uk/interpro/ - InterPro home page
• https://www.ncbi.nlm.nih.gov/protfam/?term=TIGRFAM%5Bfilter%5D - TIGRFAMs text search at NCBI
• https://ftp.ncbi.nih.gov/hmm/current - FTP site with most recent versions of TIGRFAMs, as part of a larger collection

Notes and References

1. 12520025 . 2003 . Haft . DH . Selengut . JD . White . O . The TIGRFAMs database of protein families . 31 . 1 . 371–3 . 165575 . Nucleic Acids Research . 10.1093/nar/gkg128.
2. 17151080 . 2007 . 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 . 35 . Database issue . D260–4 . 10.1093/nar/gkl1043 . 1781115 . Nucleic Acids Research.
3. 23197656 . 2012 . Haft . DH . Selengut . JD . Richter . RA . Harkins . DM . Basu . MK . Beck . E . TIGRFAMs and Genome Properties in 2013 . 41 . Database issue . D387-95 . 10.1093/nar/gks1234 . 3531188 . Nucleic Acids Research.
4. 20180275 . 2009 . Eddy . SR . A new generation of homology search tools based on probabilistic inference . 23 . 1 . 205–11 . Genome Informatics. International Conference on Genome Informatics.
5. Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A . etal. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. . Nucleic Acids Res . 2021 . 49 . D1 . D1020–D1028 . 33270901 . 10.1093/nar/gkaa1105 . 7779008 .