Nucleic Acids Research Advance Access originally published online on December 6, 2006
Nucleic Acids Research 2007 35(Database issue):D260-D264; doi:10.1093/nar/gkl1043
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Nucleic Acids Research, 2007, Vol. 35, Database issue D260-D264
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
TIGR, Bioinformatics Department 9712 Medical Center Drive, Rockville, MD 20850, USA
*To whom correspondence should be addressed. Tel: +1 301 795 7566; Fax: +1 301 838 0208; Email: selengut{at}tigr.org
Received September 18, 2006. Revised November 3, 2006. Accepted November 3, 2006.
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.
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