The TIGRFAMs database of protein families

By Daniel H. Haft, Jeremy D. Selengut, Owen White. Nucleic Acids Res., 2003

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View Paper: https://www.semanticscholar.org/paper/17891bdbfec1950f7c361db96dca043cfbf54769

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Citations in the corpus

Database resources of the National Center for Biotechnology Information (2006, methodology): “The CDD (61) contains >46000 PSI-BLAST-derived Position Specific Score Matrices representing domains taken from the Simple Modular Architecture Research Tool (62), Pfam (63), TIGRFAM (64) and from domain alignments derived from COGs and Protein Clusters.”
InterPro: the integrative protein signature database (2008, methodology): “Since then, six other member databases have also joined and their data has been integrated: SMART (6), TIGRFAMs (7), PIRSF (8), SUPERFAMILY (9), PANTHER (10) and Gene3D (11).”
Database resources of the National Center for Biotechnology Information (2011, methodology): “The CDD (56) contains over 40 000 PSI-BLAST-derived position-specific score matrices representing domains taken from the simple modular architecture research tool (Smart) (57), Pfam (58), TIGRFAM (59), and from domain alignments derived from COGs and Protein Clusters.”
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes (2006, background): “TIGRFAMs was last described in Nucleic Acids Research in 2003 (2).”
MaGe: a microbial genome annotation system supported by synteny results (2006, background): “Examples of commonly used annotation platforms are given by commercial systems, such as ERGO (7) or Pedant-Pro (successor of PEDANT), and open source systems, such as Artemis (8), GenDB (9) or Manatee (TIGR, unpublished).”
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (2015, methodology): “Pfam and TIGRFAMs families were considered redundant if they matched the same genes in >90% of the finished IMG genomes, in which case only the Pfam gene was used as a marker.”
InterPro, progress and status in 2005 (2004, methodology): “InterPro (1) integrates into one resource the major protein signatures databases: PROSITE (2), which uses regular expressions and profiles, PRINTS (3), which uses position-specific scoring matrix-based (PSSM-based) fingerprints, ProDom (4), which uses automatic sequence clustering, and Pfam (5), SMA”
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes (2005, neutral): “org/TIGRFAMs) [31].”
The comprehensive microbial resource (2000, background): “Trusted protein families: these families currently include JCVI’s TIGRFAM protein family models (10) and Pfams (11), both built on Hidden Markov Models (HMMs).”
TIGRFAMs and Genome Properties in 2013 (2012, background): “We previously introduced the term ‘ equivalog ’ to describe a relationship of conserved function among homologs (3), noting that the term ‘ ortholog ’ is doubly wrong since orthology does not imply conserved function and laterally transferred genes ( xenologs ) may be equivalogs.”
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 (2006, neutral): “32 http://www.sanger.ac.uk/Software/Pfam/ (34). 33 http://www.tigr.org/TIGRFAMs/ ( 35 ).”