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35:(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.
66:. 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
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and PGAP genome annotation pipelines. Active curation and revision of TIGRFAMs models continues at NCBI, but the creation of TIGRFAMs models
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142:"TIGRFAMs and Genome Properties: Tools for the assignment of molecular function and biological process in prokaryotic genomes"
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has ended, as newly constructed HMMs from the RefSeq group receive different designations when added to NCBIFAMs.
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Selengut, JD; Haft, DH; Davidsen, T; Ganapathy, A; Gwinn-Giglio, M; Nelson, WC; Richter, AR; White, O (2007).
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267:"RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation"
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TIGRFAMs was produced originally at The
Institute for Genomic Research (TIGR) and its successor,
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Eddy, SR (2009). "A new generation of homology search tools based on probabilistic inference".
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Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A; et al. (2021).
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Haft, DH; Selengut, JD; Richter, RA; Harkins, DM; Basu, MK; Beck, E (2012).
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Genome
Informatics. International Conference on Genome Informatics
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https://www.ncbi.nlm.nih.gov/protfam/?term=TIGRFAM%5Bfilter%5D
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https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/
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62:(NCBI). TIGRFAMs remains a member database in
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60:National Center for Biotechnology Information
313:: CS1 maint: multiple names: authors list (
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93:"The TIGRFAMs database of protein families"
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58:(JCVI), but it moved in April 2018 to the
376:This bioinformatics-related article is a
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91:Haft, DH; Selengut, JD; White, O (2003).
23:designed to support manual and automated
191:"TIGRFAMs and Genome Properties in 2013"
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338:https://www.ebi.ac.uk/interpro/
46:package written by Sean Eddy.
346:- TIGRFAMs text search at NCBI
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380:. You can help Knowledge by
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201:(Database issue): D387-95.
29:multiple sequence alignment
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152:(Database issue): D260–4.
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56:J. Craig Venter Institute
27:. Each entry includes a
195:Nucleic Acids Research
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97:Nucleic Acids Research
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427:Biological databases
340:- InterPro home page
334:- TIGRFAMs home page
283:10.1093/nar/gkaa1105
42:, TIGRFAMs uses the
277:(D1): D1020–D1028.
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33:hidden Markov model
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78:References
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50:History
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72:per se
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