Genome Data Storage via 2D Alignment Segmentation
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Solution Overview
Problem
The rapid increase in DNA sequence data volumes poses challenges in efficiently storing and retrieving genetic data, impacting scientific progress due to inefficiencies in existing storage and retrieval methods.
Innovation Solution
A method involving a processing device that receives genome files, generates a two-dimensional alignment file, separates it into groups, transposes and compresses these groups using the Flate compression algorithm, and stores them in a genome data store, allowing for efficient storage and retrieval of genetic sequence data.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If genome files are stored in traditional formats, then data can be stored, but storage space is wasted and retrieval efficiency is low
Solution Approach 1:
The alignment file is divided into multiple groups based on reference sequence intervals. Each group contains aligned genetic sequences for a specific interval, allowing selective retrieval of only the needed portions rather than loading entire files, thus improving retrieval efficiency and reducing storage overhead.
Solution Approach 2:
The patent transforms the traditional one-dimensional storage format into a two-dimensional grouped structure where one dimension represents reference sequence intervals and the other represents genetic sequences. This dimensional reorganization enables efficient random access to specific genomic regions while improving compression ratios.
2Quantity of substance
If alignment files are compressed to save space, then storage efficiency improves, but decompression time increases
Solution Approach 1:
By dividing the alignment file into multiple smaller groups, each group can be independently compressed and decompressed. When retrieving data, only the specific groups containing the needed genetic sequences need to be decompressed, significantly reducing the total decompression time compared to decompressing the entire file.
Solution Approach 2:
The system decompresses only the necessary portions (specific groups) rather than the entire alignment file. This partial action approach maintains high compression ratios for storage while minimizing decompression time by processing only the required data segments.
3Speed
If entire alignment files are loaded for retrieval, then complete data is available, but memory usage increases and access speed decreases
Solution Approach 1:
The alignment file is segmented into multiple groups corresponding to different reference sequence intervals. This segmentation allows the system to load and process only the specific groups needed for a given query, reducing memory usage and improving access speed by avoiding loading unnecessary data into memory.
Data Source
AI summary
A method includes receiving, by a processing device, a plurality of genome files. Each genome file corresponds to a different sample and defining a genetic sequence. The method also includes generating, by the processing device, a two-dimensional alignment file based on the genome files and a reference sequence. A first dimension of the alignment file corresponds to individual genetic sequences and each of the genetic sequences is aligned with respect to the reference sequence along a second dimension of the alignment file. The method includes separating, by the processing device, the alignment file into a plurality of groups and storing the groups in a non-transitory genome data store. Each group contains segments of the genetic sequences of two or more of the genomic files.