System, method and computer program for non-binary sequence comparison
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 system for sequence analysis, comprising:
an analysis module, adapted to calculate a non-binary similarity score between a first nucleotide sequence and a second nucleotide sequence; and
an output in communication with the analysis module for outputting the similarity score to a user;
wherein said analysis module comprises:
an align sequences module adapted to align a target sequence to a base sequence and to display an alignment report;
an ω 0 module adapted to calculate an ω 0 score for a sequence and to display said ω 0 score;
a query repeat module adapted to locate multiple occurrences of said target sequence in said base sequence and to display said multiple occurrences;
a query omega repeats module adapted to determine when repeated nucleotides are duplicates; and
a calculate slopes module adapted to calculate a slope for each nucleotide position in said base sequence and to display a slopes report.
2. The system of claim 1 , wherein said align sequences module is further adapted to perform at least one of reversing said base sequence, reversing a mod, aligning said base and said target to a shortest length, calculating an alignment percentage, or calculating an omega similarity score.
3. The system of claim 1 , wherein said compare sequences
module is further adapted to perform at least one of:
reversing said base sequence;
reversing said target sequence;
reversing a mod; and
calculating an ω 0 value for each of said base and said target sequences.
4. A system for sequence analysis, comprising:
an analysis module, adapted to calculate a non-binary similarity score between a first nucleotide sequence and a second nucleotide sequence;
an output in communication with the analysis module for outputting the similarity score to a user; and a plot module;
wherein said plots module comprises:
a spectral array module, adapted to plot aligning coefficients for a base sequence and a target sequence;
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
an ω N module adapted to calculate ω N for said base sequence and to display a plot of said ω N .
5. The system of claim 4 , wherein said spectral array module is further adapted to:
calculate an ω N value for radial compare; and
extract aligning coefficients.
6. The system of claim 4 , wherein said single strand module is further adapted to calculate an ω N value for said base sequence and said target sequence.