Rapid detection of conserved regions in protein sequences using wavelets

Published date : 08 Feb 2004

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.

type
Journal Paper
journal
In-Silico Biology 2004;4(2):133-48
pubmed
15107019
Url
http://www.bioinfo.de/isb/2004040013/
Impact Factor
NIL