TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

By Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle G. Giglio, W. Nelson, Alexander R. Richter, Owen White. Nucleic Acids Res., 2006

304 citations recorded by the source corpus.

TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe ‘equivalog’ families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at and .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46a886b5ef266c19719c6935936a7a0be70835ce

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Citations in the corpus

CDD: conserved domains and protein three-dimensional structure (2012, methodology): “We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI’s Protein Clusters database for providing such vital resources.”
TIGRFAMs and Genome Properties in 2013 (2012, background): “TIGRFAMs has grown by over 40% since the previous database update paper (5), from 3000 to 4284 models.”
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families (2009, methodology): “The 'family' definition adopted in the B6 database is similar to the 'equivalog family' definition of TIGRFAM [16], while a single family in PFAM [17] typically corresponds to many different families in our database.”
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, methodology): “For TIGRfam, the noise cutoff ( −− cug_nc) is used, with hits below the trusted cutoff and at/above the noise cutoff flagged as “ marginal ” .”
The Ensembl gene annotation system (2016, background): “Any candidate lincRNA containing a substantial open reading frame (ORF) (covering 35% or more of its length) and either Pfam or TIGRFAM (89) protein domains will be rejected.”
IMG 4 version of the integrated microbial genomes comparative analysis system (2013, methodology): “Function-based comparison of genomes is provided by the ‘Abundance Proﬁle Overview’ and ‘Function Proﬁle’ tools that allow comparing the relative abundance of protein families (COGs, Pfams, TIGRfams) and functional families (enzymes) across genomes.”
IMG ER: a system for microbial genome annotation expert review and curation (2009, unknown): “Genes are assigned various annotations based on functional resources, such as COG clusters (Tatusov et al., 2003), Pfam (Finn et al., 2008), TIGRfam (Selengut et al., 2007), and Gene Ontology (Gene Ontology Consortium, 2008).”
A Bioinformatician's Guide to Metagenomics (2008, methodology): “Computationally intensive tasks can also be bypassed by profile scans using profile databases such as TIGRFAM, PFAM, COGS, and InterProScan.”
CDD: a Conserved Domain Database for the functional annotation of proteins (2010, methodology): “The authors thank the authors of Pfam, SMART, COG, TIGRFAM and NCBI’s Protein Clusters database, and Figure 1.”
IMG: the integrated microbial genomes database and comparative analysis system (2011, background): “IMG generated annotations consist of protein family and domain characterizations based on COG clusters and functional categories (10), Pfam (11), TIGRfam and TIGR role categories (12), InterPro domains (13), Gene Ontology (GO) terms (14) and KEGG Ortholog (KO) terms and pathways (15).”
InterPro in 2011: new developments in the family and domain prediction database (2011, methodology): “The InterPro database integrates predictive models, or signatures, from multiple, diverse source repositories: Pfam (1), PRINTS (2), PROSITE (3), SMART (4), ProDom (5), PIRSF (6), SUPERFAMILY (7), PANTHER (8), CATHGene3D (9), TIGRFAMs (10) and HAMAP (11).”