TIGRFAMs and Genome Properties in 2013 - PubMed (original) (raw)

. 2013 Jan;41(Database issue):D387-95.

doi: 10.1093/nar/gks1234. Epub 2012 Nov 28.

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TIGRFAMs and Genome Properties in 2013

Daniel H Haft et al. Nucleic Acids Res. 2013 Jan.

Abstract

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.

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Figures

Figure 1.

Figure 1.

Example of a TIGRFAMs web page. The TIGRFAMs homepage and all its web pages have five links located on the left navigational sidebar. These go to the TIGRFAMs Home page itself, a glossary of key terms used in TIGRFAMs, a complete listing of all models (4284 in release 13.0), the TIGRFAMs FTP Site, and a page with links to additional resources, including rapid searching of a protein sequence against HMM libraries. The page shown in the figure is summary page for a single TIGRFAMs entry, the Mb-OB3b-class methanobactin precursor family TIGR04071. Each summary page provides details about a single TIGRFAM, including cutoffs, HMM length, references and any assigned GO terms. The summary page also displays links to Genome Properties, if any, associated with that HMM. Users can view and download the HMM seed alignment through the HMM Seed Alignment link found on the left-hand side of the HMM Summary page. The TIGRFAMs complete listing page (not shown) displays accessions and functional names for all models, as well as length, isology type and EC number.

Figure 2.

Figure 2.

Example of a Genome Properties Definition Page. The Genome Properties home page provides three links on the left navigation sidebar: Genome Properties List, Top Level Genome Properties and Search CMR Genome Properties. The Genome Properties List shows all current Genome Properties along with their property type and property name. Clicking on a Genome Property will display the Genome Property Definition page. The Definition Page for GenProp0962 (‘methanobactin biosynthesis, Mb-OB3b family’) is illustrated. The Genome Property Definition page displays the property’s name, description, parent/child/sibling properties, literature references and associated GO terms. The components of the property are listed with the step names, and whether or not the step is required (used to evaluate completeness). The evidence required to detect that a component has been found is described, usually the accession of a TIGRFAMs HMM with a working link to HMM Summary Page. Users can browse through the Genome Properties through the Top Level Genome Properties page linked on the home page. Users traverse through the properties by first selecting a top level property (e.g. Metabolism, Taxonomy). Associated parent, child and sibling properties are displayed for selection. The Search CMR Properties link directs users to the CMR genome property search.

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