TIGRFAMs is a database of

protein families A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be c ...

designed to support manual and automated genome annotation. Each entry includes a

multiple sequence alignment Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis an ...

and

hidden Markov model A hidden Markov model (HMM) is a Markov model in which the observations are dependent on a latent (or ''hidden'') Markov process (referred to as X). An HMM requires that there be an observable process Y whose outcomes depend on the outcomes of X ...

(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 Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is cur ...

, TIGRFAMs uses the HMMER package written by Sean Eddy.

History

TIGRFAMs was produced originally at The Institute for Genomic Research (TIGR) and its successor,

J. Craig Venter Institute The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Ge ...

(JCVI), but it moved in April 2018 to the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

(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. 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.

References

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 Biological databases {{bioinformatics-stub