title: TLFAM--a new set of protein family databases.
abstract: 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.
authors.affiliation: TimeLogic Corporation, Incline Village, Nevada 89451, USA. martyg@timelogic.com
authors.forename: Martin
authors.initials: M
authors.lastname: Gollery
authors.forename: David
authors.initials: D
authors.lastname: Rector
authors.forename: Jim
authors.initials: J
authors.lastname: Lindelien
mesh_terms: D030562:Databases, Protein; D016680:Genome, Bacterial; D008390:Markov Chains