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:
a computer system 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,
wherein said non-binary similarity score is calculated by pairing nucleotides of said first nucleotide sequence with nucleotides of said second nucleotide sequence, obtaining a similarity score for each base pair between said first nucleotide sequence and said second nucleotide sequence, and combining similarity scores of all base pairs between said first nucleotide sequence and said second nucleotide sequence, wherein the similarity score for a base pair s i /t i is a non-binary score that is calculated by counting the number of atoms present in the nucleotide s i that are not present in the nucleotide t i .
2. The system of claim 1 , wherein the similarity score for a base pair is a first value if the nucleotides in said base pair are the same, a second value if the nucleotides in said base pair are different but are both purines or pyrimidines, or a third value if one nucleotide in said base pair is a purine and another nucleotide in said base pair is a pyrimidine, and wherein the first, second and third values are different from each other.
3. The system of claim 2 , wherein the second value or the third value is further modified by a degree of differences between the chemical structure of the nucleotides in the base pair.
4. The system of claim 1 , further comprising a graphical user interface (GUI) that comprises a report module adapted to provide reports on loaded sequences; a file management module adapted to manage sequence files; and a plot module adapted to provide sequence analysis plots.
5. The system of claim 4 , wherein the GUI further comprising a user options module adapted to provide user preferences.
6. The system of claim 4 , wherein said file management module comprises:
a load sequence module, adapted to load at least one sequence file;
a flush active sequence module, adapted to flush a sequence file from a memory; and
a flush loaded sequence module, adapted to flush a loaded sequence file from said memory.
7. The system of claim 6 , wherein said load sequence module comprises:
a loaded sequence display module, adapted to generate and display a summary report notebook page when a sequence is loaded, wherein said summary report notebook page is adapted to display a sequence file name and a number of sequences.
8. The system of claim 4 , wherein said report module is adapted to generate and display at least one of:
a sequence summary;
a listing of the contents of each loaded sequence, or
statistical information about each loaded sequence.
9. The system of claim 1 , wherein said analysis module comprises a single-strand DNA analysis module and a multi-strand DNA analysis module.