Encoding/decoding method, encoder/decoder, storage method and device

Patent metadata

Field	Value
Publication number	US-12494268-B2
Application number	US-202016858295-A
Country	US
Kind code	B2
Filing date	Apr 24, 2020
Priority date	Oct 25, 2017
Publication date	Dec 9, 2025
Grant date	Dec 9, 2025

Abstract

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.

First claim

What is claimed is:

1 . An encoding method, comprising:
transcoding information to be encoded into a first binary code sequence and a second binary code sequence, using a processor; encoding the first binary code sequence and the second binary code sequence, wherein the first and second binary code sequence have the same number of bits, into an encoded sequence of the information to be encoded, using the processor, the encoded sequence composed of multiple of four different kinds of symbols, wherein the four different kinds of symbols are four kinds of deoxyribonucleotides of adenine (A), cytosine (C), guanine (G), and thymine (T) and the encoded sequence is a nucleic acid sequence composed of the four kinds of deoxyribonucleotides; splitting the nucleic acid sequence into a plurality of sequence fragments; adding an index identifier to each of the plurality of sequence fragments, the index identifier of a corresponding sequence fragment comprising position information of the corresponding sequence fragment, wherein the index identifier of the corresponding sequence fragment is a DNA sequence; and synthesizing the sequence fragments into nucleic acid fragments as an encoding result, wherein the encoding comprises: 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 a first bit of the encoded sequence;
wherein determining the current bit of the encoded sequence comprises:
determining a first candidate symbol group of the current bit of the encoded sequence based on the current first bit of the first binary code sequence according to a first mapping relationship, the first candidate symbol group comprising two of the four different kinds of symbols;
determining a second candidate symbol group of the current bit of the encoded sequence based on the current bit of the second binary code sequence and the previous bit of the encoded sequence according to a second mapping relationship, the second candidate symbol group comprising two of the four different kinds of symbols, wherein the first mapping relationship and the second mapping relationship are configured to ensure that the first candidate symbol group and the second candidate symbol group comprise one identical symbol; and
determining the identical symbol as the current bit of the encoded sequence.

2 . The encoding method according to claim 1 , wherein the encoding comprises:
determining the 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; wherein the determining of the first bit of the encoded sequence comprises:
determining a first candidate symbol group of the first bit of the encoded sequence based on the first bit of the first binary code sequence according to a first mapping relationship, the first candidate symbol group comprising two of the four different kinds of symbols;
determining a second candidate symbol group of the first bit of the encoded sequence based on the first bit of the second binary code sequence and the reference symbol according to a second mapping relationship, the second candidate symbol group comprising two of the four different kinds of symbols, wherein the first mapping relationship and the second mapping relationship are configured to ensure that the first candidate symbol group and the second candidate symbol group comprise one identical symbol; and
determining the identical symbol as the first bit of the encoded sequence.

3 . The encoding method according to claim 2 , wherein:
the first mapping relationship is a correspondence between the first bit or the current bit of the first binary code sequence and a symbol in the first candidate symbol group, the symbols in the first candidate symbol group comprising two of A, C, G, and T, the second mapping relationship is a correspondence between the first bit of the second binary code sequence, as well as the reference symbol, and a symbol of the second candidate symbol group, or a correspondence between the current bit and the previous bit of the second binary code sequence and a symbol of the second candidate symbol group, the symbols of the second candidate symbol group comprising two of A, C, G, and T.

4 . The encoding method according to claim 1 , further comprising:
transcoding the information to be encoded into a binary code; and extracting the first binary code sequence and the second binary code sequence from the binary code.

5 . The encoding method according to claim 1 , further comprising:
decoding the encoded sequence into the first binary code sequence and the second binary code sequence, wherein, the first binary code sequence is obtained by the following steps: decoding two of the four different kinds of symbols comprised in the encoded sequence to 0 and the other two of the four different kinds of symbols to 1 according to the first mapping relationship to obtain the first binary code sequence; and wherein the second binary code sequence is obtained by the following steps: determining a current bit of the second binary code sequence based on a current bit and a previous bit of the encoded sequence according to the second mapping relationship, the current bit of the encoded sequence being a bit other than the first bit of the encoded sequence.

6 . The encoding method according to claim 5 , wherein the encoded sequence is obtained by the following steps:
sequencing each nucleotide fragment to obtain the sequence fragments; according to an index identifier of each sequence fragment, obtaining position information of each sequence fragment; and according to the position information, assembling the sequence fragments into the encoded sequence.

7 . The encoding method according to claim 5 , further comprising:
combining the binary code sequences obtained by decoding into a binary code; and transcoding the binary code into corresponding information.

Assignees

• Bgi Shenzhen

Inventors

• Huang Xiaoluo
• Chen Shihong
• Lin Tao
• Chen Tai
• Shen Yue
• Xu Xun
• Yin Ye
• Yang Huanming

Classifications

• H03M7/40

  Conversion to or from variable length codes, e.g. Shannon-Fano code, Huffman code, Morse code · CPC title

• G16B30/20

  Sequence assembly · CPC title

• H03M7/02

  Conversion to or from weighted codes, i.e. the weight given to a digit depending on the position of the digit within the block or code word · CPC title

• G16B50/00 Primary

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title