TIGRFAMs: a protein family resource for the functional identification of proteins

By Daniel H. Haft, Brendan J. Loftus, Delwood L. Richardson, Fan Yang, Jonathan A. Eisen, Ian T. Paulsen, Owen White. Nucleic Acids Res., 2001

490 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/74ee39c8bb789b3e89e47f87cb1e7b33bb4184bb

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Citations in the corpus

UniProt: the Universal Protein knowledgebase (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18).”
The Universal Protein Resource (UniProt) (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (14), PROSITE (15), PRINTS (16), ProDom (17), SMART (18), PIRSF (19), Superfamily (20) and TIGRFAMs (21).”
RefSeq: an update on prokaryotic genome annotation and curation (2017, background): “The definition comes from TIGR-FAMs, where equivalog -level models are marked as such (26).”
The Pfam protein families database (2007, methodology): “As well as providing searches of the Pfam HMMs, the UK web site now offers the option to search against SMART (15) and TIGRFAM (16) HMM collections.”
The RAST Server: Rapid Annotations using Subsystems Technology (2008, background): “Hence, the basic principles underlying FIGfams are quite similar to those corresponding to the lowest-level PIR families [17] or the TIGRfam equivalogs [15].”
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales (2015, methodology): “A PSI-BLAST search [39] against the profiles available in the current version of the CDD (Conserved Domain Database) [40] was used to find the closest hits from arCOGs to pfam [41], conserved domain families [40], and tigrfams [42].”
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems (2014, background): “Much more complex features can be defined, including exchangeable genes, distant genes and component-specific parameters (File S1). doi:10.1371/journal.pone.0110726.g001 2012) [11,23].”
The InterPro Database, 2003 brings increased coverage and new features (2003, background): “Subsequently SMART (6) and TIGRFAMs (7) have joined the Consortium.”
The comprehensive microbial resource (2000, background): “Over 50 different tools are available on the CMR, broken into seven major categories: Searches: Searches allow users to find genes, genomes, sequences, or text from data stored in the CMR. Searches to find genes based on annotation (i.e. locus identifier, functional name, gene symbol), alternate acc”
The TIGRFAMs database of protein families (2003, background): “We have previously (1) defined the term ‘equivalog’ to describe the relationship of proteins conserved in function since their last common ancestor.”
The genome of M. acetivorans reveals extensive metabolic and physiological diversity. (2002, background): “…code for synthesis of extracellular polysaccharides such as lipopolysaccharides, S-layer glycoproteins, and methanochondroitin because pathways for the biosynthesis of all three involve sequential addition of UDP-PPmonosaccharides to a glycan chain (Hartmann and Konig 1989; Kandler and Konig 1998).”
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. (2002, methodology): “These ORFs were searched against TIGRFAM (Haft et al ., 2001) and PFAM hidden Markov models, and also against a non-redundant protein database.”
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 (2003, background): “This is an integrated resource of protein families, domains and sites which amalgamates the efforts of the member databases which are currently PROSITE (23), PRINTS (24), Pfam (25), ProDom (26), SMART (27) and TIGRFAMs (28).”
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. (2003, background): “families, domains, and sites that combines the complementary efforts of the PROSITE (Falquet et al. 2002), PRINTS (Attwood et al. 2002), Pfam (Bateman et al. 2002), ProDom (Corpet et al. 2000), SMART (Letunic et al. 2002), and TIGRFAMs (Haft et al. 2001) databases.”