System, method and computer program for non-binary sequence comparison
View Patent ↗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.
1. A computer-implemented method for nucleotide sequence analysis, comprising:
reading a first sequence file using one or more processors; and
calculating a slope value (Ω) for a nucleotide in a first sequence of the first sequence file using the one or more processors,
wherein the slope value reflects (1) the difference between said nucleotide and a nucleotide to the right of said nucleotide in the first sequence and (2) the difference between a nucleotide to the left of said nucleotide and said nucleotide in the first sequence.
2. The method of claim 1 , wherein slope value (Ω) is calculated based on the following formula:
Ω k =S k /S k+1 −S k−1 /S k
wherein k represents the position of the nucleotide in the first sequence, S k /S k+1 represents the Table 2 value of the nucleotide pair at k and k+1 positions, and S k−1 /S k represents the Table 2 value of the nucleotide pair at k−1 and k position.
3. The method of claim 2 , wherein the calculating step is repeated for each of the nucleotide positions in the first sequence.
4. The method of claim 3 , further comprising:
displaying a slopes report for the first sequence.
5. The method of claim 4 , wherein the slopes report is displayed by displaying the slope value of each nucleotide in the first sequence as a zero, a negative sign or a positive sign under each nucleotide.
6. The method of claim 4 , wherein the slopes report is displayed by plotting the position of each nucleotide against the slope value of the nucleotide.
7. The method of claim 4 , further comprising:
reading a second sequence file;
calculating a slope value (Ω) for each nucleotide in a second sequence of the second sequence file, and
displaying a slopes report for the second sequence.
8. The method of claim 7 , further comprising:
comparing the slopes report for the first sequence to the slopes report for the second sequence.