TLFAM--a new set of protein family databases

OMICS. 2002;6(1):35-7. doi: 10.1089/15362310252780825.


PFAM is a popular and effective database of Hidden Markov Models (HMMs), which represent a wide range of protein families. Here, we introduce TLFAM as a more specific set of HMM databases. Analyses of bacterial genomes using TLFAM-Pro show better scores, E-values, and alignment lengths than those using the more generalized PFAM. Since PFAM will still find hits that TLFAM-Pro will not, we recommend that they be used jointly, rather than exclusively. This method provides the best features of both databases. This method has been extended to a number of other organism types, such as archaea, and the databases are freely available to interested researchers.

MeSH terms

  • Databases, Protein*
  • Genome, Bacterial
  • Markov Chains