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US 2013/0297640 A1Published application
System, method and computer program for non-binary sequence comparison
OwnerJeffrey Marcus Clarkinventor
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Abstract
A system and method for performing non-binary comparison of biological sequences includes a new measure ω0, 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.
Claims6
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 (ωo) 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 ωN;
- performing a radial comparison;
- extracting alignment coefficients;
- and
- plotting said alignment coefficients.
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