Patent ID: 7424369
Filing Date: 2008-09-09
Classification: G16B

Abstract:
1. A method for use in sequence data analysis comprising: providing a multiple sequence alignment of a plurality of sequences, wherein the multiple sequence alignment comprises a column of aligned amino acids and/or gaps for each horizontal position of the multiple sequence alignment; providing a plurality of numerical physical-chemical property (PCP) descriptors for each amino acid based on a plurality of physical-chemical properties thereof, wherein each of the plurality of numerical PCP descriptors corresponds to one of “N” eigenvectors used in defining the amino acids in terms of physical-chemical properties; describing each amino acid in the multiple sequence alignment quantitatively in terms of the plurality of PCP descriptors as a series of “N” eigenvectors resulting in “N” PCP described sequence alignments, wherein each PCP described sequence alignment corresponds to and is defined with numerical PCP descriptors which correspond to one of the “N” eigenvectors, and further wherein each PCP described sequence alignment comprises a plurality of columns corresponding to the columns of the multiple sequence alignment; analyzing each of the PCP described sequence alignments, on a column by column basis, to generate conservation property data for each column, wherein the conservation property data for each column comprises an average value for the numerical PCP descriptors in the column and a standard deviation associated with the average value, and a relative entropy value for the column; analyzing the conservation property data for each of the PCP described sequence alignments to detect consecutive horizontal positions of the multiple sequence alignment where the physical-chemical properties are conserved based on at least the relative entropy determined for each column; defining one or more PCP motifs in the multiple sequence alignment based at least on the detection of consecutive horizontal positions of the multiple sequence alignment where the physical-chemical properties are conserved according to at least one eigenvector; and outputting one or more of the defined PCP motifs to at least one of a user, a display, and a file user readable format.