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A Structured Evolutionary Algorithm for Identification of Transcription Factor Binding Sites in Unaligned DNA Sequences

Shripal Vijayvargiya, Pratyoosh Shukla

Identification of Transcription Factor Binding Sites (TFBS) also called as motifs, from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we propose an evolutionary approach to identify transcription factor binding sites. This approach is based on the structured genetic algorithm. In this approach an individual is represented as a structured tree that help us to find variable length motifs. A simple GA can find only fix length motif where as proposed method can find variable length motifs. We applied this approach on various data sets and the results show that it can find correct result both effective and efficient for binding sites.