A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS)

  • Authors:

  • Chetan Kumar;Nishith Kumar;Sarani Rangarajan;Narayanaswamy Balakrishnan;Kanagaraj Sekar

  • Affiliations:

  • Bioinformatics Centre (Centre of excellence in Structural Biology, and Bio-computing),;Bioinformatics Centre (Centre of excellence in Structural Biology, and Bio-computing),;Bioinformatics Centre (Centre of excellence in Structural Biology, and Bio-computing),;Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India 560 012;Bioinformatics Centre (Centre of excellence in Structural Biology, and Bio-computing), and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India 560 012

  • Venue:
  • PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
  • Year:
  • 2008

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Abstract

Sequence motifs occurring in a particular order in proteins or DNA have been proved to be of biological interest. In this paper, a new method to locate the occurrences of up to five user-defined motifs in a specified order in large proteins and in nucleotide sequence databases is proposed. It has been designed using the concept of quantifiers in regular expressions and linked lists for data storage. The application of this method includes the extraction of relevant consensus regions from biological sequences. This might be useful in clustering of protein families as well as to study the correlation between positions of motifs and their functional sites in DNA sequences.