TIGRFAMs
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.
Like Pfam, TIGRFAMs uses the HMMER package written by Sean Eddy.[4] TIGRFAMs is produced at the J. Craig Venter Institute. It is one of 11 member databases in InterPro. The current version of TIGRFAMs, release 15.0, has 4488 models.
References
- ^ Haft, DH; Selengut, JD; White, O (2003). "The TIGRFAMs database of protein families". Nucleic Acids Research. 31 (1): 371–3. doi:10.1093/nar/gkg128. PMC 165575. PMID 12520025.
- ^ Selengut, JD; Haft, DH; Davidsen, T; Ganapathy, A; Gwinn-Giglio, M; Nelson, WC; Richter, AR; White, O (2007). "TIGRFAMs and Genome Properties: Tools for the assignment of molecular function and biological process in prokaryotic genomes". Nucleic Acids Research. 35 (Database issue): D260–4. doi:10.1093/nar/gkl1043. PMC 1781115. PMID 17151080.
- ^ Haft, DH; Selengut, JD; Richter, RA; Harkins, DM; Basu, MK; Beck, E (2012). "TIGRFAMs and Genome Properties in 2013". Nucleic Acids Research. 41 (Database issue): D387-95. doi:10.1093/nar/gks1234. PMC 3531188. PMID 23197656.
- ^ Eddy, SR (2009). "A new generation of homology search tools based on probabilistic inference". Genome informatics. International Conference on Genome Informatics. 23 (1): 205–11. PMID 20180275.
External links
- http://www.jcvi.org/cgi-bin/tigrfams/index.cgi - TIGRFAMs home page
- http://hmmer.janelia.org/search/hmmscan - high speed search of protein sequences against Pfam or TIGRFAMs libraries at Janelia Farm Research Campus
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