Genome Compression via Reference Indexing and Difference Data
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Solution Overview
Problem
Current genome compression methods face challenges in efficiently selecting a matching reference genome and in accessing specific genome data without decompressing the entire genome, leading to suboptimal data storage and transmission efficiency.
Innovation Solution
A method that selects a reference genome from a database based on phenotypic traits or predefined sequences, builds an index on the reference genome's segments, aligns the genome to identify difference data, and generates a compressed genome including the index and difference data, allowing for rapid access to specific genome segments without decompressing the entire genome.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If the entire genome is compressed and stored, then complete genome data is preserved, but storage space consumption is excessive
Solution Approach 1:
The patent extracts only the difference data between the target genome and reference genome, storing only the variable portions rather than the complete genome sequence. This extraction approach preserves essential genetic information while dramatically reducing storage requirements by eliminating redundant identical sequences.
Solution Approach 2:
The patent applies local quality by differentiating between conserved regions (stored in reference genome) and variable regions (stored as difference data). Each region is handled according to its specific characteristics, with high-similarity regions referenced externally and divergent regions stored locally, optimizing storage efficiency based on local data properties.
2Loss of information
If the entire compressed genome is decompressed for access, then complete genome information is available, but decompression time and computational resources are excessive
Solution Approach 1:
The patent segments the genome into reference portions (from reference database) and difference portions (stored compression data). This segmentation allows selective decompression where only the necessary difference data needs to be processed while the reference portion remains accessible in its original form, significantly reducing decompression time for specific queries.
Solution Approach 2:
The patent implements partial decompression by allowing access to genome information without decompressing the entire compressed dataset. Users can query and access specific regions by combining reference genome data with relevant difference data, performing only the minimal necessary decompression action required for the specific information need.
3Loss of substance
If a reference genome is selected based on comprehensive similarity analysis, then compression ratio is maximized, but the complexity of reference selection increases
Solution Approach 1:
The patent performs preliminary action by pre-processing and indexing the reference genome database before compression operations. This includes pre-calculating similarity metrics and organizing reference sequences in an optimized structure, which simplifies the reference selection process during actual compression by providing pre-computed comparison data and reducing real-time computational complexity.
Data Source
AI summary
The present invention relates to a method and apparatus for genome compression and decompression. In one embodiment of the present invention, there is a method for genome compression, including: selecting from a reference database a reference genome that matches the genome; building an index based on positions of the reference genome's multiple segments in the reference genome; aligning the genome with the reference genome based on the multiple segments so as to identify difference data between the genome and the reference genome; and generating a compressed genome, the compressed genome including at least the index and the difference data. In other embodiments, there is provided an apparatus for genome compression. Further, there is a method and apparatus for decompressing the genome that has been compressed using the above method and apparatus.