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OMICS. 2002;6(1):35-7.

TLFAM--a new set of protein family databases.

Author information

1
TimeLogic Corporation, Incline Village, Nevada 89451, USA. martyg@timelogic.com

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.

PMID:
11881833
DOI:
10.1089/15362310252780825
[Indexed for MEDLINE]

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