Application of the Codon-based Scoring Method in Motif Detection

A RNA or DNA sequence motif is a short sequence found within a particular nucleic acid sequence families. Most amino acid and nucleic acid sequences have some level of functional or struc-tural similarities. These similarities are mostly represented by short, contiguous sequences called motif. Motif discovery is an important aspect of molecular biology. This is because the knowl-edge of these sequences helps determine their structural proper-ties, signal sites and/or ligand-binding sites. In most cases, de-pending on the function of the motif, these contiguous regions can be highly conserved with an homology of nearly 100%. Sev-eral algorithms have been proposed for the discovery of motifs. In this paper, the codon-based scoring method is employed to de-tect motifs and with their invariants. The result obtained shows the reliability and robustness of the method as motifs are dis-covered irrespective of their length and position in a sequence. General Terms: Motif, , similarity measure, clusterin