Coding and decoding method for integrity check and error correction of DNA sequence

Abstract

The invention discloses a coding and decoding method for DNA sequence integrity check and error correction. The coding and decoding method comprises a DNA integrity coding algorithm and a DNA integrity decoding algorithm. A coder uses a DNA integrity coding algorithm to code a DNA sequence to be subjected to integrity protection, and uses codon degeneracy to embed integrity verification information without changing corresponding amino acids, and does not introduce additional bases. After the synthesized DNA sequence is subjected to a biochemical process, a sequencing result has the possibility of introducing base insertion, deletion and replacement. A decoder can use a DNA integrity decoding algorithm to perform verification and error correction on a sequencing result. If the sequencing result of the sequence is error-free, the decoding algorithm must feed back that the sequencing result is error-free; if an error exists in the sequence sequencing result, the decoding algorithm judges that the error exists in an extremely high probability and corrects the error, and the recovered sequence capable of passing through the decoding algorithm is a decoding result; and if the error digits exceed the error digits willing to undertake by the decoders, the serious errors are prompted to be unrecoverable.

Description

technical field [0001] The invention belongs to the field of bioinformatics, and in particular relates to a coding and decoding method for DNA sequence integrity check and error correction. Background technique [0002] Bioinformatics is an interdisciplinary subject that uses the methods of applied mathematics, informatics, statistics and computer science to study biological problems. As early as the 1860s, the academic community proposed the concept of DNA-based data storage. After nearly 60 years of development, research related to DNA storage has gradually become an important branch in the field of bioinformatics. [0003] In terms of storage media for DNA storage, there are mainly two categories: in vivo-based information storage and in vitro information storage. The early enlightening research was limited by the level of DNA sequencing and synthesis technology at that time, using in vivo information storage methods, using living cells (such as bacteria, etc.) to carry ...

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Problems solved by technology

In order to provide such support, the existing methods usually make certain concessions, such as: having to sacrifice a part of the base sequence or introduce an additional base sequence as the carrier of the integrity check code, resulting in a decrease in information capacity or destroying the original sequence Another example: Most of the improved schemes based on the existing mature error-correcting codes occupy too many bases on the one hand, and on the other hand, the error-correcting ability is limited by factors such as the code distance. Designed as a fixed value, that is, at the beginning of the scheme design, the error correction capability is strictly limited, so it is difficult to expand to continue to explore its error correction capability

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