Systematic DNA-Binding Domain Classification of Transcription Factors

Philip Stegmaier[1] (
Alexander E. Kel[1] (
Edgar Wingender[1],[2] (

[1]BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany
[2]Department of Bioinformatics, Medical School, University of Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, Germany


Based on the manual annotation of transcription factors stored in the TRANSFAC database, we developed a library of hidden Markov models (HMM) to represent their DNA-binding domains and used it for a comprehensive classification. The models constructed were applied on the UniProt/Swiss-Prot database, leading to a systematic classification of further DNA-binding protein entries. The HMM library obtained can be used to classify any newly discovered transcription factor according to its DNA-binding domain and, thus, to generate hypotheses about its DNA-binding specificity.

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Japanese Society for Bioinformatics