Convolutional Coding for DNA Storage Insertion-Deletion Errors
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Solution Overview
Problem
DNA storage systems face significant delays due to the time-consuming process of sequencing multiple strands to correct insertion and deletion errors, which are prevalent in DNA storage and break traditional error correction codes.
Innovation Solution
Implement a system using two or more component convolutional and trellis codes that are time-interlaced to detect and correct insertion and deletion errors, allowing for reduced sequencing by identifying and adjusting symbol locations, thereby enabling traditional error correction codes to handle substitution errors.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If multiple sequencing operations are performed to correct insertion and deletion errors, then reliability is improved, but loss of time worsens
Solution Approach 1:
The patent segments the error correction process into two distinct phases: first using insertion/deletion correcting codes (such as convolutional codes with specific trellis structures) to handle insertion and deletion errors, then using traditional substitution correcting codes to handle substitution errors. This segmentation allows each code type to specialize in correcting specific error types, improving overall efficiency and reducing the number of sequencing operations needed compared to using only traditional repetition-based methods.
Solution Approach 2:
The patent changes the parameters of the coding scheme by using codes with specific properties (such as convolutional codes with constraint length k≥2 and specific generator polynomials) that are optimized for detecting and correcting insertion and deletion errors. This parameter optimization allows the system to achieve the same reliability with fewer sequencing operations, thereby reducing time loss.
2Reliability
If traditional error correction codes are used, then substitution errors are corrected, but insertion and deletion errors cannot be corrected
Solution Approach 1:
The patent implements a universal error correction system that can handle multiple types of errors (insertion, deletion, and substitution) by combining different coding schemes. The first code is designed to correct insertion and deletion errors, while the second code corrects substitution errors. This multi-functional approach allows the system to address all major error types that occur in DNA storage, making it versatile and adaptable to various error conditions.
Solution Approach 2:
The patent introduces an intermediary processing step where the output of the first code (which corrects insertion and deletion errors) is passed to the second code (which corrects substitution errors). This intermediary approach allows each code to focus on its specialized error type while working together to provide comprehensive error correction, bridging the gap between the limitations of individual code types.
3Reliability
If the same DNA strand is sequenced multiple times to estimate a final string, then insertion and deletion errors are reduced, but productivity decreases
Solution Approach 1:
The patent applies preliminary error correction coding to the DNA sequence before sequencing. By encoding the data with insertion/deletion correcting codes first, the system prepares the data in advance to withstand sequencing errors. This preliminary action reduces the need for multiple re-sequencing operations, thereby improving productivity while maintaining sequence accuracy.
Solution Approach 2:
The patent implements a feedback mechanism where the decoded sequence is checked for errors and, if necessary, re-sequenced only for specific portions that failed error correction. This selective feedback approach is more efficient than re-sequencing entire strands multiple times, improving productivity while maintaining high sequence accuracy.
Data Source
AI summary
This disclosure describes systems and methods for detecting multiple insertion and deletion errors in the presence of substitution errors in a signal (such as a sequenced DNA string). A convolutional code that includes two or more component convolutional codes is used for encoding. Each of the two or more component convolutional codes generates only a subset of all possible outputs of the convolutional code. The subsets of the two or more component convolutional codes are disjoint from each other. Only one of the two or more convolutional codes is active at any given time. The two or more convolutional codes together define a super code. The two or more convolutional codes are time interlaced within the super code, and the super code defines the convolutional code. A trellis that includes two or more component trellises designed based on the two or more component convolutional codes is used for decoding.