Oligomer Indexing via Key Patterns for Variable Separation Mapping
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Solution Overview
Problem
Existing methods are inadequate for accurately and efficiently mapping short oligomer sequences with variable separation distances to a reference sequence in genetic research, as they lack the computational speed and cost-effectiveness required for precise location identification.
Innovation Solution
The development of searchable indexes generated by applying key patterns to a reference sequence, which correspond to predicted sequence relationships within polyoligomer data sets, allowing for the identification of potential locations through key mapping.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing mapping approaches are used for short oligomer sequences, then the mapping can be performed with current methods, but the accuracy and efficiency of mapping is insufficient due to variable separation distances
Solution Approach 1:
The patent segments the oligomer mapping problem into two distinct phases: (1) building a comprehensive index structure from reference sequences that pre-computes all possible oligomer patterns with their separation distances, and (2) performing rapid lookup of experimental oligomers against this pre-built index. This segmentation allows the computationally intensive work to be done once during index creation, enabling fast and accurate mapping during actual analysis without repeating expensive computations.
Solution Approach 2:
The patent applies preliminary action by pre-computing and storing all possible oligomer sequences and their corresponding separation distances in a reference index before actual mapping is needed. This pre-processing step creates a comprehensive lookup table that captures all valid oligomer patterns, allowing subsequent mapping operations to simply query this pre-computed structure rather than performing complex real-time calculations, thereby achieving both high accuracy and computational efficiency.
2Productivity
If short oligomer sequences with variable separation distances are mapped using existing methods, then mapping can be attempted, but computational cost and time consumption increase significantly
Solution Approach 1:
The patent divides the mapping task into two segments: an offline phase where a comprehensive index of all possible oligomer patterns with variable separation distances is pre-computed and stored, and an online phase where experimental oligomers are rapidly matched against this pre-built index. This segmentation eliminates the need to perform expensive computational searches during actual mapping operations, achieving high mapping speed while minimizing computational time loss.
Solution Approach 2:
The patent creates a comprehensive copy of all possible oligomer patterns and their separation distance relationships in a pre-computed reference index. Instead of performing complex calculations during mapping, the system simply queries this pre-created copy of the reference space, enabling rapid matching of experimental oligomers against all possible patterns without re-computing the underlying relationships, thereby achieving fast mapping with minimal time consumption.
3Adaptability or versatility
If traditional mapping approaches are used, then simple sequence matching can be performed, but the ability to handle variable separation distances between oligomers is inadequate
Solution Approach 1:
The patent applies preliminary action by pre-computing and storing all possible oligomer patterns with their separation distances in a structured reference index before mapping is needed. This pre-computation phase handles the complexity of variable separation distances by capturing all valid patterns in advance, allowing the mapping phase to simply query this pre-organized structure. The index structure, while complex in construction, provides simple and efficient queries during actual mapping operations.
Solution Approach 2:
The patent changes the parameter representation by organizing the reference index around oligomer patterns and their separation distances rather than simple sequence positions. This parameter transformation allows the system to naturally handle variable separation distances by storing them as explicit attributes in the index structure, enabling flexible querying of oligomers with any separation distance pattern without requiring complex runtime calculations.
Data Source
AI summary
Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.