Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency

: Finding motifs and the corresponding binding sites is a critical and challenging problem in studying the process of gene expression. String and matrix representations are two popular models to represent a motif. However, both representations share an important weakness by assuming that the occurrence of a nucleotide in a binding site is independent of other nucleotides. More complicated representations, such as HMM or regular expression, exist that can capture the nucleotide dependency. Unfortunately, these models are not practical (with too many parameters and require many known binding sites). Recently, Chin and Leung introduced the SPSP representation which overcomes the limitations of these complicated models. However, discovering novel motifs in SPSP representation is still a NP-hard problem. In this paper, based on our observations in real binding sites, we propose a simpler model, the Dependency Pattern Sets (DPS) representation, which is simpler than the SPSP model but can st...

• Type: Conference
• Year: 2008
• Where: APBC
• Authors: Francis Y. L. Chin, Henry C. M. Leung, Man-Hung Siu, Siu-Ming Yiu
• Keywords: APBC 2008, Binding Sites, Bioinformatics, Nucleotide Dependency, SPSP Representation