Systematic DNA-binding domain classification of transcription factors.

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.