Encoding and storing text using DNA sequences

Patent metadata

Field	Value
Publication number	US-11017170-B2
Application number	US-201816143671-A
Country	US
Kind code	B2
Filing date	Sep 27, 2018
Priority date	Sep 27, 2018
Publication date	May 25, 2021
Grant date	May 25, 2021

Abstract

Text can be encoded into DNA sequences. Each word from a document or other text sample can be encoded in a DNA sequence or DNA sequences and the DNA sequences can be stored for later retrieval. The DNA sequences can be stored digitally, or actual DNA molecules containing the sequences can be synthesized and stored. In one example, the encoding technique makes use of a polynomial function to transform words based on the Latin alphabet into k-mer DNA sequences of length k. Because the whole bits required for the DNA sequences are smaller than the actual strings of words, storing documents using DNA sequences may compress the documents relative to storing the same documents using other techniques. In at least one example, the mapping between words and DNA sequences is one-to-one and the collision ratio for the encoding is low.

First claim

The invention claimed is:

1. A system comprising:
a storage device;
a non-transitory computer-readable medium including computer program code for DNA encoding of text; and
a processing device communicatively coupled to the storage device and the non-transitory computer-readable medium, wherein the processing device is configured for executing the computer program code to perform operations comprising:
receiving a word to be converted into a DNA sequence;
determining a value of a polynomial function based on the word, wherein the determining the value of the polynomial function comprises converting each letter of the word to a letter number and calculating a sum of a position-th power of each letter number for each letter multiplied by the letter number;
obtaining a remainder of a modulus of the value of the polynomial function;
converting the remainder of the modulus into the DNA sequence;
storing the DNA sequence in the storage device;
synthesizing a DNA molecule of the DNA sequence; and
storing the DNA molecule.

2. The system of claim 1 wherein the DNA sequence comprises a nucleotide sequence of a length corresponding to a power of two used to determine the modulus.

3. The system of claim 2 wherein the nucleotide sequence further comprises a mapping of two-digit groups from a binary value of the remainder.

4. The system of claim 1 further comprising a stored DNA dictionary to provide the DNA sequence for a plurality of words.

5. The system of claim 1 wherein the determining the value of the polynomial function based on the word further comprises converting each letter of the word to uppercase.

6. The system of claim 1 wherein the converting the remainder of the modulus into the DNA sequence comprises:
separating a binary value of the remainder into a plurality of two-digit groups; and
mapping the plurality of two-digit groups into a nucleotide sequence.

7. The system of claim 1 wherein the DNA sequence comprises a 10-mer sequence.

8. A method comprising:
receiving a word to be converted into a DNA sequence;
determining a value of a polynomial function based on the word, wherein the determining the value of the polynomial function comprises converting each letter of the word to a letter number and calculating a sum of a position-th power of each letter number for each letter multiplied by the letter number;
obtaining a remainder of a modulus of the value of the polynomial function;
converting the remainder of the modulus into the DNA sequence;
storing the DNA sequence in a storage device; and
synthesizing a DNA molecule of the DNA sequence and storing the DNA molecule.

9. The method of claim 8 wherein the DNA sequence comprises a nucleotide sequence of a length corresponding to a power of two used to determine the modulus.

10. The method of claim 9 wherein the nucleotide sequence further comprises a mapping of two-digit groups from a binary value of the remainder.

11. The method of claim 8 wherein the determining the value of the polynomial function based on the word further comprises converting each letter of the word to uppercase.

12. The method of claim 8 wherein the converting the remainder of the modulus into the DNA sequence comprises:
separating a binary value of the remainder into a plurality of two-digit groups; and
mapping the plurality of two-digit groups into a nucleotide sequence.

13. The method of claim 8 wherein the DNA sequence comprises a 10-mer sequence.

14. A non-transitory computer-readable medium including computer program code executable by a processor to cause the processor to perform operations, the operations comprising:
receiving a word to be converted into a DNA sequence;
determining a value of a polynomial function based on the word, wherein determining the value of the polynomial function comprises converting each letter of the word to a letter number and calculating a sum of a position-th power of each letter number for each letter multiplied by the letter number;
obtaining a remainder of a modulus of the value of the polynomial function;
converting the remainder of the modulus into the DNA sequence;
storing the DNA sequence in a storage device; and
synthesizing a DNA molecule of the DNA sequence, and storing the DNA molecule.

15. The non-transitory computer-readable medium of claim 14 wherein the DNA sequence comprises a nucleotide sequence of a length corresponding to a power of two used to determine the modulus.

16. The non-transitory computer-readable medium of claim 15 wherein the nucleotide sequence further comprises a mapping of two-digit groups from a binary value of the remainder.

17. The non-transitory computer-readable medium of claim 14 the operations further comprise accessing a stored DNA dictionary to provide the DNA sequence when the word is one of a plurality of words having a corresponding DNA sequence stored in the DNA dictionary.

18. The non-transitory computer-readable medium of claim 14 wherein the determining the value of the polynomial function based on the word further comprises converting each letter of the word to uppercase.

19. The non-transitory computer-readable medium of claim 14 wherein the converting the remainder of the modulus into the DNA sequence comprises:
separating a binary value of the remainder into a plurality of two-digit groups; and
mapping the plurality of two-digit groups into a nucleotide sequence.

20. The non-transitory computer-readable medium of claim 14 wherein the DNA sequence comprises a 10-mer sequence.

Assignees

• At & T Ip I Lp

Inventors

• Yin Changchuan

Classifications

• G06F40/284 Primary

  Lexical analysis, e.g. tokenisation or collocates · CPC title

• G06F40/123 Primary

  Storage facilities · CPC title

• G06F40/242

  Dictionaries · CPC title

• H03M7/6011

  Encoder aspects · CPC title

• H03M7/55

  Compression Theory, e.g. compression of random number, repeated compression · CPC title