Dynamic Seed Size Hash Table Genome Sequence Alignment
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Solution Overview
Problem
Current genome sequence alignment methods using hash tables face challenges in balancing accuracy and speed, with large seed sizes leading to alignment failures and small seed sizes increasing computation time, while requiring more memory resources.
Innovation Solution
The method involves using multiple hash tables with different seed sizes, starting with a large seed size for alignment and progressing to smaller sizes if necessary, aligning the target nucleotide sequence to the position with the smallest difference below a threshold, and reporting failure only when no alignment is possible in the smallest seed size.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If a large seed size is used in hash table-based genome sequence alignment, then alignment speed increases, but alignment accuracy decreases leading to more alignment failures
Solution Approach 1:
The patent dynamically adjusts the seed size during the alignment process. It starts with a large seed size for fast initial matching, then adaptively reduces the seed size when mismatches are detected, allowing the system to maintain high speed for perfect matches while ensuring accuracy for sequences with variations.
Solution Approach 2:
The invention changes the seed size parameter based on the matching results. When a large seed size fails to produce sufficient matches, the system modifies the parameter by using smaller seed sizes in subsequent hashing operations, thereby balancing speed and accuracy through parameter optimization.
2Reliability
If a small seed size is used in hash table-based genome sequence alignment, then alignment accuracy increases, but computation time increases
Solution Approach 1:
The patent performs preliminary action by first attempting alignment with a large seed size before resorting to smaller seed sizes. This preliminary fast search filters out obvious matches, and only when necessary does the system proceed to more computationally intensive smaller seed size searches, thereby reducing overall computation time.
Solution Approach 2:
The alignment process is segmented into multiple stages with different seed sizes. The system divides the search into hierarchical levels: first level uses large seed sizes for quick filtering, and subsequent levels use smaller seed sizes only for the remaining candidates, thus segmenting the computational workload to minimize total time.
3Reliability
If multiple hash tables with different seed sizes are used, then alignment reliability increases, but device complexity increases
Solution Approach 1:
The patent implements multi-functionality by designing a unified hash table structure that can accommodate multiple seed sizes. Rather than creating separate independent systems for each seed size, the invention makes a single hash table structure serve multiple purposes by dynamically adjusting the seed size parameter, thereby reducing overall system complexity.
Data Source
AI summary
An apparatus for genome sequence alignment attempts a search for the hash tables to align a target nucleotide sequence, from a hash table having a large seed size to a hash table having a small seed size, and when there is at least one matched seed to the target nucleotide sequence on a hash table, aligns the target nucleotide sequence by using candidate positions from the hash table without further hash table searching.