Philip Stegmaier (email@example.com)
Alexander E. Kel (firstname.lastname@example.org)
Edgar Wingender, (email@example.com)
BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany
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.