Oligomer Sequence Mapping via Key Substitution
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Solution Overview
Problem
Existing methods are inadequate for accurately mapping short oligomer sequences with variable separation distances to a reference genome, as they fail to robustly identify data errors, mutations, or polymorphisms while being inefficient in terms of computational speed and cost.
Innovation Solution
The method involves generating keys from oligomer sequences, modifying these keys by substituting bases, and comparing them to a reference index to determine candidate locations, using techniques such as single or combined base substitutions, insertions, and deletions to efficiently map oligomer sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing mapping approaches are used for short oligomer sequences with variable spacing, then the mapping process is simple, but the accuracy and robustness in identifying mutations or polymorphisms deteriorates
Solution Approach 1:
The patent segments the oligomer mapping problem into multiple processing stages: generating initial keys from oligomer sequences, creating modified keys through systematic base substitutions, and comparing against a reference index. This segmentation allows each stage to handle specific aspects of the mapping challenge, improving overall accuracy while managing complexity through structured decomposition of the mapping task.
Solution Approach 2:
The patent performs preliminary actions by pre-generating a reference index from the reference genome before actual mapping occurs. This pre-computed index contains all possible key patterns and their corresponding locations, enabling faster and more accurate mapping during the actual analysis phase. The preliminary construction of the index structure facilitates robust mutation detection without adding complexity to the real-time mapping process.
2Reliability
If existing mapping approaches are used for short oligomer sequences, then the computational process is fast, but the ability to identify data errors and mutations deteriorates
Solution Approach 1:
The patent applies parameter changes by systematically varying the key patterns through base substitutions at different positions. By modifying keys to include all possible base combinations at each position, the method transforms the mapping process into a comprehensive search that reliably identifies mutations and errors. This parameter variation approach maintains computational efficiency by using structured substitution patterns rather than exhaustive random searching.
Solution Approach 2:
The patent creates multiple copies of keys with different base substitutions at various positions. These copied and modified keys are then compared against the reference index to identify matches. This copying strategy enables robust error detection by having multiple representations of the same oligomer sequence, where at least one copy is likely to match even in the presence of sequencing errors or mutations.
3Adaptability or versatility
If base substitutions are made in all positions of the key, then the coverage of possible mutations is complete, but the computational cost increases
Solution Approach 1:
The patent applies local quality by focusing base substitutions on specific positions within the key rather than uniformly substituting all positions. By identifying and prioritizing positions that are more likely to contain mutations or variations, the method achieves comprehensive mutation detection coverage while reducing computational cost by limiting substitutions to critical regions of the oligomer sequence.
Data Source
AI summary
Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.