Construction of a Functional Word Dictionary for Primate Promoter Sequences

Wataru Fujibuchi (
Minoru Kanehisa (

Institute for Chemical Research
Kyoto University
Uji, Kyoto 611


We constructed a dictionary of sequence motifs for transcription regulation with a heuristic method from a set of DNA sequences upstream of the transcription initiation site. The method first identifies weakly conserved blocks within a given region relative to the initiation site by the search and merge of six-base patterns. Then most conserved portions of these blocks are extracted by calculating the information content after similar blocks are multiply aligned. The procedure was applied to primate promoters and the result was evaluated with the Transcription Factor Database (TFD). The result will give us new biological insights into the DNA signals.