Engineering Commons^™

Finding Dna Motifs: A Probabilistic Suffix Tree Approach, Abhishek Majumdar

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

We address the problem of de novo motif identification. That is, given a set of DNA sequences we try to identify motifs in the dataset without having any prior knowledge about existence of any motifs in the dataset. We propose a method based on Probabilistic Suffix Trees (PSTs) to identify fixed-length motifs from a given set of DNA sequences. Our experiments reveal that our approach successfully discovers true motifs. We compared our method with the popular MEME algorithm, and observed that it detects a larger number of correct and statistically significant motifs than MEME. Our method is highly efficient as …