Eukaryotic promoter recognition by binding sites for transcription factors
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences pr. Lavrentyeva 10, Novosibirsk, 630090, Russia
2Istituto di Tecnologie Biomediche Avanzate, Consiglio Nazionale Delle Ricerche Milan, Italy
1 To whom correspondence should be addressed
A method for identification of eukaryotic promoters by localization of binding sites for transcription factors has been suggested. The binding sites for a range of transcription factors have been found to be distributed unevenly. Based on these distributions, we have constructed a weight matrix of binding site localization. On the basis of the weight matrix we have, in turn, designed an algorithm for promoter recognition. To increase the accuracy of the method, we have developed a routine that breaks any promoter sample into subsamples. The method to be reported on allows much better recognition accuracy than does the approach based on detection of the TA TA box. In particular, the overprediction error is three times lower following our method. The program FunSiteP recognizes promoters from newly uncovered sequences and tentatively identifies the functional class the promoters must belong to. We have introduced the notion of ‘regulatory potential’ for the degree to which any region of the sequences is similar to the real eukaryotic promoter. By making use of the potential, we have revealed putative transcription start sites and extended regions of transcription regulation.
Received on November 1, 1994; revised on April 27, 1995; accepted on April 28, 1995
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