Chapter

Pattern Recognition in Bioinformatics

Volume 6282 of the series Lecture Notes in Computer Science pp 137-148

An Algorithm to Find All Identical Motifs in Multiple Biological Sequences

  • Ashish Kishor BindalAffiliated withBioinformatics Centre (Centre of excellence in Structural Biology and Bio-computing), Indian Institute of Science
  • , R. SabarinathanAffiliated withBioinformatics Centre (Centre of excellence in Structural Biology and Bio-computing), Indian Institute of Science
  • , J. SridharAffiliated withCenter of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University
  • , D. SherlinAffiliated withBioinformatics Centre (Centre of excellence in Structural Biology and Bio-computing), Indian Institute of Science
  • , K. SekarAffiliated withBioinformatics Centre (Centre of excellence in Structural Biology and Bio-computing), Indian Institute of Science

Abstract

Sequence motifs are of greater biological importance in nucleotide and protein sequences. The conserved occurrence of identical motifs represents the functional significance and helps to classify the biological sequences. In this paper, a new algorithm is proposed to find all identical motifs in multiple nucleotide or protein sequences. The proposed algorithm uses the concept of dynamic programming. The application of this algorithm includes the identification of (a) conserved identical sequence motifs and (b) identical or direct repeat sequence motifs across multiple biological sequences (nucleotide or protein sequences). Further, the proposed algorithm facilitates the analysis of comparative internal sequence repeats for the evolutionary studies which helps to derive the phylogenetic relationships from the distribution of repeats.

Keywords

Sequence motifs nucleotide and protein sequences identical motifs dynamic programming direct repeat and phylogenetic relationships