Memory Array Bloom Filter for Parallel Genetic Sequence Alignment
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Solution Overview
Problem
Next-generation sequencing (NGS) systems generate vast numbers of reads that require significant computation time for alignment to reference sequences, necessitating improved alignment techniques.
Innovation Solution
A memory array is used to implement a Bloom filter, allowing for parallel comparison of reads to multiple reference sequences, providing absolute negatives for non-matches and reducing computation time by eliminating non-matches and allowing for further confirmation of potential matches.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of time
If traditional sequential alignment methods are used to align reads to reference sequences, then alignment accuracy can be maintained, but computation time becomes excessively long when processing millions to billions of reads
Solution Approach 1:
The patent segments the alignment process into two distinct phases: (1) a rapid filtering phase using Bloom filters to eliminate non-matching reads, and (2) a precise confirmation phase using traditional alignment algorithms only for potential matches. This segmentation allows the system to process millions of reads quickly by applying computationally intensive methods only where necessary, thereby reducing overall computation time while maintaining alignment accuracy.
Solution Approach 2:
The patent introduces Bloom filters as an intermediary data structure between the read input and the reference sequence alignment process. These Bloom filters serve as a preliminary filtering layer that rapidly identifies and eliminates non-matching reads before they undergo computationally expensive alignment operations. This intermediary mechanism enables the system to handle large volumes of reads efficiently while preserving the accuracy of final alignment results.
2Productivity
If parallel processing is implemented to reduce computation time, then alignment speed improves, but system complexity increases
Solution Approach 1:
The patent extracts the filtering function from the main alignment process and implements it using Bloom filters. This extraction allows the system to handle the high-throughput requirement separately from the accuracy-critical alignment operation. By taking out the filtering task and assigning it to a specialized data structure, the system achieves parallel processing capabilities without significantly increasing the complexity of the core alignment algorithm.
3Measurement precision
If all reads are subjected to full alignment verification, then alignment accuracy is maximized, but computation time increases significantly
Solution Approach 1:
The patent applies partial action by performing full alignment verification only on reads that pass the Bloom filter screening, rather than on all reads. The Bloom filter provides a probabilistic first layer of verification that eliminates the vast majority of non-matching reads. This approach applies the computationally intensive full alignment action selectively and partially, only where truly necessary, thereby maintaining high alignment accuracy while dramatically reducing overall computation time.
Data Source
AI summary
A memory device may be used to implement a Bloom filter. In some examples, the memory device may include a memory array to perform a multiply-accumulate operation to implement the Bloom filter. The memory device may store multiple portions of a reference genetic sequence in the memory array and compare the portions of the reference genetic sequence to a read sequence in parallel by performing the multiply-accumulate operation. The results of the multiply-accumulate operation between the read sequence and the portions of the reference genetic sequence may be used to determine where the read sequence aligns to the reference sequence.