DNA Sequence Compression via Template Difference Encoding
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Solution Overview
Problem
The vast amount of DNA sequencing data generated by modern sequencing techniques poses a significant burden in storage, computation, and communication due to the need for efficient data compression, as raw sequences are continuously produced and require real-time processing without loss or missing data.
Innovation Solution
A sequence compression method and device that compares sequences to generate a final template sequence and compress data by identifying differences, using seed tables and the minimum base-shift principle to achieve efficient data reduction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If raw sequencing data is stored and processed in full detail, then data integrity and accuracy are maintained, but storage capacity and computational resources are excessively consumed
Solution Approach 1:
The patent segments the DNA sequencing data into discrete positional information and nucleotide identity information. Instead of storing complete sequences, the system divides data into position coordinates and base call identities, allowing selective storage of only essential information while maintaining data integrity for reconstruction.
Solution Approach 2:
The patent extracts only the essential positional information and nucleotide identity data from complete sequencing reads, separating and storing only these critical elements. This extraction approach removes redundant information while preserving the core data needed for accurate sequence reconstruction and analysis.
2Quantity of substance
If compression algorithms are applied to reduce data size, then storage and communication efficiency improve, but risk of data loss or missing information increases
Solution Approach 1:
The patent performs preliminary organization of sequencing data into structured positional and identity information before compression. By pre-structuring the data with clear positional coordinates and associated nucleotide identities, the system enables lossless reconstruction without requiring storage of complete redundant sequences.
Solution Approach 2:
The patent creates a compressed representation that acts as a precise copy of the essential sequencing information. The positional data and nucleotide identities are stored in a compact format that can be accurately reconstructed into the original sequence information, ensuring no loss of critical data.
3Loss of time
If real-time processing of continuous sequencing signals is performed, then data freshness and timeliness are maintained, but computational burden and processing complexity increase
Solution Approach 1:
The patent extracts only the essential positional and identity information from continuous sequencing signals in real-time, rather than processing complete sequences. This extraction approach significantly reduces computational complexity while maintaining data freshness by processing only the critical elements as they are generated.
Solution Approach 2:
The patent segments the continuous sequencing signal processing into discrete position identification and nucleotide calling steps. This segmentation allows real-time processing of individual positional elements independently, reducing overall processing complexity while maintaining timely data generation.
Data Source
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AI summary
The invention provides a data compression method, comprising: (a) obtaining a first reading sequence and a second reading sequence from an identical source by a receiving unit; (b) comparing the first reading sequence with the second reading sequence according to a comparison condition to generate a sequence comparison result by the processor; (c) outputting a final template sequence according to the sequence comparison result by the processor; (d) comparing the final template sequence to each of the first and second reading sequences, to generate a respective difference between the final template sequence and each of the first and second reading sequences by the processor; and (e) compressing the first and second reading sequences according to the final template sequences and all generated differences between the final template sequence and the first and second reading sequences, to generate a compression file by the processor.