System, method and computer program for non-binary sequence comparison

Abstract

A system and method for performing non-binary comparison of biological sequences includes a new measure ω 0 , which is a non-binary counting measure that is used in a stand alone module called VaSSA-1. This measure obtains substantially more information about sequences and comparisons between them than is gathered by conventional bioinformatics techniques.

What is claimed is: 
     
         1 . A method for sequence analysis, comprising:
 reading a sequence file;   selecting a target sequence and a base sequence from said file;   performing a non-binary comparison between each base pair of said target and said base sequences, wherein said non-binary comparison generates a comparison value (ω o ) for each base pair;   determining a similarity between said target and said base sequences based on said comparison values; and   generating at least one of a two-dimensional spectral array plot or a two-dimensional single strand plot, wherein generating said spectral array plot comprises:
 calculating ω N ; 
 performing a radial comparison; 
 extracting alignment coefficients; and 
 plotting said alignment coefficients. 
   
     
     
         2 . The method of  claim 1 , further comprising: reversing one of said base or said target; and reversing a calculation. 
     
     
         3 . The method of  claim 1 , wherein the similarity is determined by 
       
         
           
             
               
                 
                   
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                   16 
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                   N 
                 
               
               . 
             
           
         
       
     
     
         4 . The method of  claim 1 , wherein said comparison value (ω o ) is generated using a computer system comprising an analysis module having an align sequences module adapted to align the target sequence to the base sequence and a ω o  module adapted to produce a comparison value (ω o ) based on the sequence alignment. 
     
     
         5 . The method of  claim 1 , wherein said two-dimensional spectral array plot or two-dimensional single strand plot is generated using a computer system comprising a plots module, wherein said plots module comprises: a spectral array module, adapted to plot aligning coefficients for a base sequence and a target sequence, and a single strand module adapted to plot a single strand for said base sequence and said target sequence; a slopes module adapted to calculate a slope for each nucleotide position in said base sequence and to display a plot of said slopes; and a ω N  module adapted to calculate ω N  for said base sequence and to display a plot of said ω N . 
     
     
         6 . The method of  claim 3 , wherein s i /t i  is a non-binary function representing the omega similarity score at base position i of the target sequence and the base sequence, and N is the number of nucleotides in the shorter of the two sequences being compared.