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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[1] 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.

[2] 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.

[3] 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.

[4] 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.