Nucleic Acid Sequence Identification Using Hash Table K-mer Indexing
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Solution Overview
Problem
Existing methods for identifying nucleic acid sequences from Next Generation Sequencing (NGS) data are inefficient, particularly when comparing multiple sequences, and do not adequately consider sequence position, leading to delays in therapeutic support.
Innovation Solution
The development of an improved method and system that utilizes Hash Tables to represent sequences, allowing for the selection and comparison of sequences based on k-mers and their positions, thereby enabling rapid identification of specific nucleic acid sequences and their classification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional sequence comparison methods (Needleman-Wunsch, Smith-Waterman) are used to identify nucleic acid sequences, then sequence identification accuracy is maintained, but processing time increases significantly when comparing multiple sequences
Solution Approach 1:
The patent segments sequences into k-mers (subsequences of length k) and uses these segments as indexing keys in hash tables. This segmentation allows the system to compare sequences by their constituent k-mers rather than performing full sequence alignments, dramatically reducing processing time while maintaining identification accuracy through the use of multiple k-mer lengths and scoring systems.
Solution Approach 2:
The patent replaces the mechanical sequence alignment process (Needleman-Wunsch, Smith-Waterman algorithms) with a computational hash table-based system. Instead of performing iterative dynamic programming alignments, the system uses hash tables to store and retrieve k-mer positions, enabling O(1) average-time complexity for k-mer lookups and significantly accelerating sequence identification.
2Reliability
If traditional alignment methods are used to compare sequences, then comprehensive sequence analysis is achieved, but the number of comparisons increases exponentially with the number of sequences
Solution Approach 1:
The patent performs preliminary actions by pre-processing reference sequences into hash tables containing all possible k-mers and their positions before actual sequence identification. This preliminary indexing allows the system to quickly retrieve relevant positions during identification without performing exhaustive comparisons, maintaining analysis completeness while dramatically improving efficiency.
Solution Approach 2:
The patent introduces k-mers as intermediary elements between the query sequence and the reference database. Instead of directly comparing full sequences, the system uses k-mers as mediators to find potential matches, then validates these matches using scoring systems that consider k-mer frequencies, positions, and combinations, ensuring comprehensive analysis with reduced computational burden.
3Device complexity
If sequential processing devices are used for sequence analysis, then system complexity is kept simple, but processing capacity is limited and response time increases
Solution Approach 1:
The patent changes the fundamental parameters of sequence analysis by transforming sequences into hash table structures with k-mer keys and position values. This parameter transformation enables parallel processing capabilities, as multiple k-mer lookups and score calculations can be performed simultaneously without the sequential dependencies inherent in traditional alignment algorithms, thereby increasing processing capacity while maintaining conceptual simplicity.
Data Source
AI summary
The present invention provides an improved method and system for identifying nucleic acid sequences within a set of sequences obtained by a sequencer, constructing database according to the identification of nucleic acid sequences, identifying different genus, species, sub-species, serotypes, variety of microorganism, virus, genes, or nucleic acid sequences of interest, for its use in the field of molecular biology applied to diagnosis, in hospitals, schools, industry or any place wherein this method and system is required to identify nucleic acid sequences, obtained by a sequencer. Specifically, the present invention provides an improved method and system that allow sequences to be differentiated from data obtained by nucleic acid sequencing.