DNA-based data storage and retrieval
The present disclosure generally relates to DNA-based data storage. An exemplary method for storing input data on nucleic acid comprises: converting the input data into a set of nucleotide sequences and synthesizing a set of nucleic acids comprising the set of nucleotide sequences. The converting comprises a data processing step comprising converting the input data into a binary string, and a nucleotide encoding step comprising converting the binary string using a 5-bit transcoding framework to obtain the set of nucleotide sequences.
1 . A method for storing input data on nucleic acid molecules, the method comprising:
a) converting the input data into a set of nucleotide sequences, wherein the converting comprises
i) a data processing step comprising converting the input data into a binary string and dividing the binary string into a sequence of non-overlapping 5-bit binary strings;
ii) a nucleotide encoding step comprising converting the sequence of non-overlapping 5-bit binary strings into the set of nucleotide sequences using a 5-bit transcoding framework to convert each 5-bit binary string into a corresponding 3-mer nucleotide sequence, wherein each corresponding 3-mer nucleotide sequence comprises:
a first base and a second base selected from A, T, C, and G; and
a third base selected from R and Y, wherein:
R is selected from any two of A, T, C, and G;
Y is selected from the corresponding other two of A, T, C, and G;
R and Y are chosen so that they are different from the second base immediately in front of R or Y; and
R and Y are chosen based on a GC content of the set of nucleotide sequences; and
b) synthesizing a set of nucleic acid molecules corresponding to the set of nucleotide sequences generated by converting the input data.
2 . The method of claim 1 , wherein the nucleotide encoding step further comprises converting each 5-bit binary string of the sequence of non-overlapping 5-bit binary strings into an integer ranging from 0 to 31 to obtain a string of integers.
3 . The method of claim 2 , wherein the nucleotide encoding step further comprises dividing the string of integers into a plurality of initial sub-sequence of integers having a predetermined length.
4 . The method of claim 3 , wherein the length of each of the plurality of initial sub-sequence of integers is determined based on an oligo length of a selected synthesis platform, a desired error tolerance, a size of the input data, a selected error correction code, or a combination thereof.
5 . The method of claim 3 , wherein the nucleotide encoding step further comprises adding index information to each of the plurality of the initial sub-sequences of integers to obtain a plurality of integer sub-sequences having indexes.
6 . The method of claim 5 , wherein the index information added to each of the plurality of the initial sub-sequences of integers comprises a sequence of integers, wherein the length of the sequence of integers is based on the size of the input data.
7 . The method of claim 5 , wherein the nucleotide encoding step further comprises, after adding the index information, adding redundancy data to the plurality of integer sub-sequences having indexes, thereby obtaining a plurality of integer sub-sequences having redundancy.
8 . The method of claim 7 , wherein adding redundancy data to the plurality of integer sub-sequences having indexes comprises:
creating an empty matrix, wherein the number of columns in the empty matrix is larger than the size of the plurality of integer sub-sequences having indexes, and wherein the number of rows of the empty matrix is larger than the number of integers in each of the plurality integer sub-sequences having indexes;
filling the empty matrix with the plurality of integer sub-sequences having indexes and data generated by applying an error correction coding; and
obtaining the plurality of sub-sequences having redundancy based on the filled matrix.
9 . The method of claim 8 , wherein the number of columns of the empty matrix is determined based on an oligo length of a selected synthesis platform, the type of the error correction code, a predetermined error tolerance value, a size of the plurality of integer sub-sequences having index, or a combination thereof.
10 . The method of claim 8 , wherein the number of rows of the empty matrix is determined based on an oligo length of a selected synthesis platform, a type of the error correction code, a predetermined error tolerance value, a size of the plurality of integer sub-sequences having indexes, or a combination thereof.
11 . The method of claim 8 , wherein the error correction coding is Reed-Solomon (“RS”) coding.
12 . The method of claim 11 , wherein the data generated by applying an error correction coding is generated by applying string correction of the RS coding and/or block correction of the RS coding.
13 . The method of claim 1 , wherein the input data corresponds to a compressed file.
14 . The method of claim 1 , wherein the input data corresponds to two or more files.
15 . The method of claim 1 , wherein the input data corresponds to a text file.
16 . The method of claim 1 , wherein the data processing step further comprises compressing the input data to obtain a compressed file and converting the compressed file into a binary string.