InterJournal Complex Systems, 1306
Status: Accepted
Manuscript Number: [1306]
Submission Date: 2004
Transcription Factor Binding Sites Prediction based on Sequence Similarity
Author(s): Jeong Seop Sim ,Myung Eun Lim ,Myung Geun Chung ,Soo-Jun Park

Subject(s): CX.3



The availability of the whole genome sequences of human due to the Human Genome Project makes it possible to study gene function much more efficiently. We can find or predict the functions and positions of genes by analyzing the transcriptional regulation. In this paper, we propose an algorithm of predicting TF binding sites from a given set of sequences of upstream regions of genes using suffix array and local alignment algorithm. Our algorithm based on following two assumptions: i) there tends to be a common TF that binds with each of the upstream regions of the functionally related genes, ii) a TF binds with similar DNA sequences.

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