Rapid Detection of Conserved Regions in Protein Sequences Using Wavelets

Article type: Research Article

Authors: Krishnan, Arun | Li, Kuo-Bin | Issac, Praveen

Affiliations: Bioinformatics Institute, 30 Biopolis Street, 07-01, Matrix, Singapore 138671. E-mail: {arun, kuobin, praveeni}@bii.a-star.edu.sg

Note: [] Corresponding author

Abstract: We present an algorithm to detect protein sub-structural motifs from primary sequence. The input to the algorithm is a set of aligned multiple protein sequences. It uses wavelet transforms to decompose protein sequences represented numerically by different indices (such as polarity, accessible surface area or electron-ion integration potentials of the amino acids). The numerical representation of a protein sequence has significant correlation with its biological activity, thus common motifs are expected to be observable from the wavelet spectrum. The decomposed signals are then up-sampled and similarity search techniques are used to identify similar regions across all the proteins at multiple scales. Results indicate that wavelet transform techniques are a promising approach for rapid motif detection.

Keywords: protein motif detection, wavelet analysis, conserved motifs

Journal: In Silico Biology, vol. 4, no. 2, pp. 133-148, 2004