DNA Sequence Alignment Using FM-Index Suffix Array Construction
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Solution Overview
Problem
Current DNA sequencing data processing and analysis techniques, such as next-generation sequencing (NGS), face challenges with high processing time and memory requirements, particularly for short alignments and large DNA sequences.
Innovation Solution
A method and system for DNA sequence alignment that involves generating suffixes from a reference DNA sequence, sampling and grouping strings, sorting them lexicographically, and establishing an FM-index data structure to efficiently perform alignments, reducing memory requirements and processing time.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If FM-index data structure is used to search for short DNA sequences, then alignment throughput is significantly improved, but memory space requirement becomes excessively large
Solution Approach 1:
The patent divides the reference DNA sequence into multiple suffixes by circular shifting, and further segments the suffix array construction into multiple passes. The FM-index is built incrementally by processing suffixes in groups rather than all at once, reducing peak memory requirements while maintaining alignment throughput.
Solution Approach 2:
The patent performs preliminary sorting of suffixes into a suffix array before constructing the FM-index. By pre-organizing the suffix data in sorted order, the subsequent FM-index construction requires less memory for temporary data structures, resolving the contradiction between throughput and memory usage.
2Measurement precision
If early alignment techniques like BLAST and BFAST are used, then alignment accuracy is maintained, but processing time becomes excessively long
Solution Approach 1:
The patent replaces the mechanical comparison-based alignment approaches of BLAST and BFAST with a data structure-based search mechanism. The FM-index enables logarithmic-time pattern matching by substituting linear scanning with binary search over the suffix array, dramatically reducing processing time while preserving alignment accuracy.
Solution Approach 2:
The patent changes the fundamental parameter of search complexity from linear O(n) to logarithmic O(log n) by transforming the alignment problem into a range query problem on the suffix array. This parameter change enables fast accurate search without sacrificing alignment precision.
3Measurement precision
If conventional sorting methods are used for all strings, then complete sorting accuracy is achieved, but processing time increases significantly
Solution Approach 1:
The patent segments the suffix array construction into multiple passes, where each pass sorts a subset of suffixes rather than all suffixes simultaneously. This segmentation reduces the computational burden of each sorting operation while achieving complete sorting accuracy through iterative refinement.
Solution Approach 2:
The patent performs partial sorting in each pass, sorting only the necessary portion of suffixes required for that iteration. By performing excessive sorting actions across multiple passes rather than one complete sort, the patent reduces the time complexity from O(n log n) to approximately O(n) total processing time.
Data Source
AI summary
A method for DNA sequence alignment is proposed to include steps of: generating multiple strings by acquiring foremost k number of suffixes corresponding to a reference DNA sequence; grouping the strings into multiple string groups; sorting the strings in each of the string groups to generate sorting results; obtaining sorted suffixes and a suffix array based on the sorting results; establishing FM-index data based on the sorted suffixes and the suffix array; and performing DNA sequence alignment on a target string based on the FM-index data to obtain an alignment result.