Genome Sequence Alignment Index Segmentation for Memory Efficiency
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current genome sequence alignment methods are inefficient in utilizing available memory, leading to suboptimal performance and high memory usage, especially when relying on software technologies that require large memory resources, which can be a limiting factor in general computer systems without specialized hardware.
Innovation Solution
An apparatus and method that load essential and additional indexes into memory based on available memory capacity, using a seed table and multi-location table to quickly check for exact matches in the reference genome, allowing for partial loading of indexes and prioritizing the essential parts to enhance alignment speed without requiring special hardware.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Speed
If software technology requiring large memory (e.g., hash table) is used to quickly find exact match, then alignment speed is improved, but memory usage increases to tens to hundreds of gigabytes making it difficult to execute on general computers
Solution Approach 1:
The patent divides the index into multiple segments (first index, second index, third index) that can be loaded into memory in parts. The first index is loaded entirely, while the second and third indexes are loaded partially based on available memory capacity, allowing the system to function on general computers with limited memory while still achieving fast alignment through selective use of index segments.
Solution Approach 2:
The patent applies partial loading of index segments based on available memory. Instead of requiring the complete index structure to be loaded at once, the system loads only the necessary portions (partial action) of the second and third indexes according to memory availability, enabling execution on systems with constrained resources while maintaining alignment performance.
2Speed
If hardware devices (FPGA, ASIC) are used to accelerate specific steps of sequence alignment, then alignment speed is improved, but device complexity and cost increase requiring special equipment
Solution Approach 1:
The patent creates a universal software solution that can run on general-purpose computers without requiring specialized hardware like FPGA or ASIC. The multi-index structure with selective loading provides hardware-accelerated performance through software, making the technology universally applicable to any computing platform while eliminating the need for complex hardware devices.
3Reliability
If essential index is loaded into memory for genome sequence alignment, then alignment accuracy is maintained, but available memory for additional optimization is reduced
Solution Approach 1:
The patent segments the index structure into multiple functional parts (first index for essential alignment, second and third indexes for acceleration) that can be independently loaded. This segmentation allows the essential index to be loaded completely for accuracy while additional segments are loaded partially based on remaining memory, optimizing the balance between accuracy and resource usage.
Solution Approach 2:
The patent implements dynamic loading of index segments based on available memory capacity. The system adaptively determines how much of the second and third indexes to load into memory after the first index is loaded, allowing flexible optimization of memory usage while maintaining alignment accuracy through the essential first index.
Data Source
AI summary
Disclosed herein are an apparatus and method for accelerating genome sequence alignment. The method may include loading an essential index for a reference genome into memory, loading an additional index corresponding to the amount of available memory into memory, reading a target nucleotide sequence for which genome sequence alignment is to be performed, checking whether an exact match of the target nucleotide sequence is present in the reference genome based on the additional index, and generating a result of alignment of the target nucleotide sequence using the location of the exact match of the target nucleotide sequence in the reference genome when an exact match is found.