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      The TIGRFAMs database of protein families.

      1 , ,
      Nucleic acids research
      Oxford University Press (OUP)

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          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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          Author and article information

          Journal
          Nucleic Acids Res
          Nucleic acids research
          Oxford University Press (OUP)
          1362-4962
          0305-1048
          Jan 01 2003
          : 31
          : 1
          Affiliations
          [1 ] The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. haft@tigr.org
          Article
          10.1093/nar/gkg128
          165575
          12520025
          c3db37bb-148b-4935-8c99-3393ee741818
          History

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