Embedded Reference Marks for DNA Storage Indel Correction
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Solution Overview
Problem
Current DNA data storage technologies face inefficiencies in error correction, particularly for insertion and deletion errors, which traditional Reed-Solomon error correction codes struggle to address effectively.
Innovation Solution
The implementation of embedded reference marks at predetermined intervals in DNA oligos, combined with Viterbi algorithms to traverse correlation matrices, allows for the correction of insertion and deletion errors before applying other error correction techniques.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If Reed-Solomon error correction codes are applied to individual oligos, then error correction capability is provided, but insertion and deletion errors cannot be corrected effectively
Solution Approach 1:
The patent segments the oligo sequence into multiple segments by inserting reference marks at predetermined intervals. Each segment can be independently analyzed for insertions and deletions, allowing the system to handle these errors locally rather than requiring global error correction mechanisms. This segmentation enables the Viterbi algorithm to efficiently traverse and compare sequences between reference marks.
Solution Approach 2:
Reference marks serve as intermediary elements between the beginning and end of oligos, providing known sequence anchors that facilitate the detection and correction of insertions and deletions. These intermediary reference points enable the correlation matrix approach to function effectively by providing fixed points for sequence alignment and comparison.
2Device complexity
If traditional error correction methods are used, then processing complexity is reduced, but data recovery accuracy for insertion and deletion errors deteriorates
Solution Approach 1:
The patent performs preliminary actions by inserting reference marks into the oligo sequence before sequencing and error correction processing. These pre-placed reference marks enable subsequent algorithms to efficiently identify and correct insertions and deletions without requiring complex trial-and-error approaches, thus improving data recovery accuracy while maintaining manageable processing complexity.
Solution Approach 2:
The patent introduces a new dimensional approach by constructing a correlation matrix that adds a temporal or positional dimension to the error correction process. Instead of simply comparing sequences linearly, the correlation matrix approach creates a two-dimensional structure where rows and columns represent different sequence positions and potential offset values, enabling more accurate detection of insertions and deletions.
3Reliability
If reference marks are inserted at predetermined intervals, then insertion and deletion errors can be corrected, but storage capacity per oligo is reduced
Solution Approach 1:
The patent applies parameter changes by optimizing the interval between reference marks to balance error correction capability with storage capacity. By carefully selecting the predetermined interval, the system ensures sufficient reference marks for reliable error correction while minimizing the overhead and maximizing the payload capacity of each oligo. This parameter optimization resolves the contradiction between reliability and storage capacity.
Data Source
AI summary
Example systems and methods for using embedded reference marks and a correlation matrix to correct insertions and deletions for DNA data storage are described. A data unit may be encoded in oligos that include reference marks at predetermined intervals along the length of each oligo. During decoding, a comparison of reference marks from the read data of the oligo to a known reference mark pattern may be used to populate a correlation matrix. A most likely path for traversing the correlation matrix may be determined to identify offsets corresponding to insertions and deletions in the oligo, which may then be corrected during further decoding of the oligo.