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Nucleic Acids Research, 2003, Vol. 31, No. 1 371-373
© 2003 Oxford University Press

The TIGRFAMs database of protein families

Daniel H. Haft*, Jeremy D. Selengut and Owen White

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Email: haft{at}tigr.org

ABSTRACT

TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references and pointers to related TIGRFAMs, Pfam and InterPro models. These models are designed to support both automated and manually curated annotation of genomes. TIGRFAMs contains models of full-length proteins and shorter regions at the levels of superfamilies, subfamilies and equivalogs, where equivalogs are sets of homologous proteins conserved with respect to function since their last common ancestor. The scope of each model is set by raising or lowering cutoff scores and choosing members of the seed alignment to group proteins sharing specific function (equivalog) or more general properties. The overall goal is to provide information with maximum utility for the annotation process. TIGRFAMs is thus complementary to Pfam, whose models typically achieve broad coverage across distant homologs but end at the boundaries of conserved structural domains. The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs.


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