Abstract:
: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 http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Selengut JD,Haft DH,Davidsen T,Ganapathy A,Gwinn-Giglio M,Nelson WC,Richter AR,White Odoi
10.1093/nar/gkl1043subject
Has Abstractpub_date
2007-01-01 00:00:00pages
D260-4issue
Database issueeissn
0305-1048issn
1362-4962pii
gkl1043journal_volume
35pub_type
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