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.
Stegmaier
Philip
P
BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany. pst@biobase.de
Kel
Alexander E
AE
Wingender
Edgar
E
D001665:Binding Sites; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000145:classification*; D016208:Databases, Factual; D030562:Databases, Protein; D016678:Genome; D019077:Helix-Turn-Helix Motifs; D020218:Response Elements; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D020825:T-Box Domain Proteins; D014157:Transcription Factors / Q000737:chemistry / Q000145:classification
D004268:DNA-Binding Proteins; D020825:T-Box Domain Proteins; D014157:Transcription Factors