TIGRFAMs and Genome Properties in 2013

By Daniel H. Haft, Jeremy D. Selengut, Roland A. Richter, Derek M. Harkins, Malay Kumar Basu, Erin Beck. Nucleic Acids Res., 2012

526 citations recorded by the source corpus.

TIGRFAMs, available online at http://www.jcvi.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.jcvi.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature.

Subfields: Molecular Biology, Renewable Energy, Sustainability and the Environment

View Paper: https://www.semanticscholar.org/paper/3ee7d214192130a46316a59c75723de936545431

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Citations in the corpus

Prokka: rapid prokaryotic genome annotation (2014, unknown): “This sequence file is the only mandatory parameter to the software.”
Identification of protein secretion systems in bacterial genomes (2015, methodology): “Eight profiles for T9SS were extracted from PFAM or TIGRFAM 91,106 .”
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley (2015, methodology): “To gain further insights on the molecular mechanisms driving the functional diversification of the barley rhizosphere microbiota, the gene families identified in the assembled barley metagenome were annotated based on matches to TIGRFAM 398 Cell Host & Microbe 17, 392–403, March 11, 2015 ª2015 The A”
InterProScan 5: genome-scale protein function classification (2014, methodology): “The large-scale mode makes use of a single relational database to store information about sequences (either nucleotide or protein sequences), predictive models and InterPro content, and the matches predicted by InterProScan.”
RefSeq: an update on prokaryotic genome annotation and curation (2017, methodology): “A limitation of HMMs used in annotation, at NCBI and probably elsewhere, is that the shared collection of models in HMM libraries available for download and distribution, including Pfam, TIGRFAMs and the new NCBIfam-PRK set, have tended to focus on the largest, most-widespread families.”