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 ...
designed to support manual and automated
genome annotation. 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
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families.
Uses
...
, 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 G ...
(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.
[ ] 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
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