Discovering Motifs in DNA Sequences: A Suffix Tree Based Approach

Abstract

Motif discovery also known as motif finding is a challenging problem in the field of bioinformatics that deals with various computational and statistical techniques to identify short patterns, often referred to as motifs that corresponds to the binding sites in the DNA sequence for transcription factors. Owing to the recent growth of bioinformatics, a good number of algorithms have come into limelight. This paper proposes a competent algorithm that extracts binding sites in set of DNA sequences for transcription factors, using successive iterations on the sequences provided. The motif we work on are of unknown length, un-gapped and non-mutated. The algorithm uses suffix trie for finding such sites. In this approach the first sequence is used as base for constructing the suffix trie and is mapped with other sequences which results in extraction of the motif. Additionally, this algorithm can also be applied to related problems in the field of data mining, pattern detection, etc.