Rapid detection of conserved regions in protein sequences using wavelets.
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.
Krishnan
Arun
A
Bioinformatics Institute, 30 Biopolis Street, 07-01, Matrix, 138671, Singapore. arun@bii.a-star.edu.sg
Li
Kuo-Bin
KB
Issac
Praveen
P
D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005583:Fourier Analysis; D015233:Models, Statistical; D008962:Models, Theoretical; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods; D012984:Software