DNA Encoding Scheme for High-Density Low-Repetition Storage
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Solution Overview
Problem
Traditional storage technologies face limitations in storage density and are unable to avoid high GC or AT repetition rates in DNA storage, leading to difficulties in reading sequence information during sequencing.
Innovation Solution
An encoding method that combines two binary code sequences into a single encoded sequence using four different symbols, with specific mapping relationships to ensure high storage density and avoid high GC or AT repetition rates, followed by synthesis into nucleic acid fragments for storage and subsequent decoding.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If two binary code sequences are encoded into one encoded sequence using four different symbols, then storage density is improved, but the complexity of encoding and decoding processes increases
Solution Approach 1:
The patent merges two binary code sequences into a single encoded sequence by combining their bits at corresponding positions. Each position in the encoded sequence represents a pair of bits (one from each binary sequence), enabling double the storage density. The four different symbols (A, C, G, T) are used to represent the four possible combinations of two binary bits (00, 01, 10, 11), effectively combining information from two sources into one compact representation.
Solution Approach 2:
The patent changes the parameter representation by mapping binary bit pairs to nucleotide symbols. Instead of storing binary sequences directly, the system transforms them into a four-symbol alphabet (A, C, G, T) where each symbol encodes two bits of information. This parameter transformation enables higher storage density while maintaining a systematic encoding/decoding framework that manages the increased complexity through structured mapping relationships.
2Measurement precision
If specific mapping relationships are used to avoid high GC or AT repetition rates, then decoding accuracy is improved, but the complexity of determining mapping relationships increases
Solution Approach 1:
The patent applies local quality by making the mapping relationship between bit pairs and nucleotide symbols context-dependent. Instead of using a fixed global mapping, the system selects different mapping relationships based on local sequence characteristics, specifically aiming to avoid high GC or AT repetition rates in certain regions. This allows the encoding to adapt to local requirements, improving decoding accuracy by preventing problematic repetition patterns that could confuse the decoding process.
Solution Approach 2:
The patent performs preliminary action by pre-determining appropriate mapping relationships before the actual encoding process. The system analyzes the binary sequences and selects mapping relationships that will avoid creating excessive GC or AT repetitions in the encoded nucleotide sequence. This advance planning ensures that the encoded sequence has optimal properties for accurate decoding, while the complexity of determining these relationships is managed through systematic evaluation of mapping options.
Data Source
AI summary
An encoding/decoding method, an encoder/decoder, and a storage method and device are provided. The encoding method comprises: determining a first bit of the encoded sequence based on a first bit of the first binary code sequence, a first bit of the second binary code sequence, and a reference symbol, the reference symbol being any one of the four different kinds of symbols; determining a current bit of the encoded sequence based on a current bit of the first binary code sequence, a current bit of the second binary code sequence, and a previous bit of the encoded sequence, the current bit of the encoded sequence being a bit other than the first bit of the encoded sequence.