Gene alignment technology

1 . A gene alignment method implemented by a computer system comprising an optical computing chip, the gene alignment method comprising:

obtaining reference gene fragments from a gene database based on a to-be-tested gene sequence, wherein the gene database comprises a reference gene sequence, wherein the reference gene sequence comprises the reference gene fragments, and wherein the reference gene fragments match some bases of the to-be-tested gene sequence;

inputting the to-be-tested gene sequence and the reference gene fragments into the optical computing chip;

performing a first optical alignment of the to-be-tested gene sequence and the reference gene fragments using the optical computing chip;

determining, based on an output result of the first optical alignment, that a similarity degree between the to-be-tested gene sequence and a first gene fragment in the reference gene fragments is less than a first threshold and greater than a second threshold;

obtaining a plurality of reference gene subsequences from the reference gene sequence, wherein the reference gene subsequences comprise a first reference gene subsequence;

inputting the to-be-tested gene sequence and the first reference gene subsequence into the optical computing chip;

performing a second optical alignment of the to-be-tested gene sequence and the first reference gene subsequence to obtain a first similarity degree between the to-be-tested gene sequence and the first reference gene subsequence;

making a determination that the first similarity degree is greater than a third threshold and less than a fourth threshold, wherein the fourth threshold is not greater than the first threshold;

obtaining, in response to the determination, a first to-be-tested gene subsequence and a second to-be-tested gene subsequence based on the to-be-tested gene sequence, wherein some bases of the first to-be-tested gene subsequence are the same as some bases of the second to-be-tested gene subsequence;

inputting the first to-be-tested gene subsequence and the first reference gene subsequence into the optical computing chip;

performing a third optical alignment of the first to-be-tested gene subsequence and the first reference gene subsequence to obtain a second similarity degree;

inputting the second to-be-tested gene subsequence and the first reference gene subsequence into the optical computing chip; and

performing a fourth optical alignment of the second to-be-tested gene subsequence and the first reference gene subsequence to obtain a third similarity degree.

2 . The gene alignment method of claim 1 , further comprising recording, when the second similarity degree is greater than the fourth threshold, a location of the first reference gene subsequence in the reference gene sequence.

3 . The gene alignment method of claim 1 , further comprising:

obtaining, when the third similarity degree is greater than the third threshold and less than the fourth threshold, a first to-be-tested gene subsequence unit and a second to-be-tested gene subsequence unit based on the second to-be-tested gene subsequence, wherein some bases of the first to-be-tested gene subsequence unit are the same as some bases of the second to-be-tested gene subsequence unit;

inputting the first to-be-tested gene subsequence unit and the first reference gene subsequence into the optical computing chip;

performing a fifth optical alignment of the first to-be-tested gene subsequence unit and the first reference gene subsequence;

inputting the second to-be-tested gene subsequence unit and the first reference gene subsequence into the optical computing chip; and

performing a sixth optical alignment of the second to-be-tested gene subsequence unit and the first reference gene subsequence.

4 . The gene alignment method of claim 1 , further comprising:

determining, based on the output result, that a first reference gene fragment of the reference gene fragments matches the to-be-tested gene sequence; and

recording a location of the first reference gene fragment in the reference gene sequence.

5 . The gene alignment method of claim 1 , wherein inputting the to-be-tested gene sequence and the reference gene fragments comprises:

separately performing optical encoding on the to-be-tested gene sequence and the reference gene fragments; and

separately inputting optical code of the to-be-tested gene sequence and optical code of the reference gene fragments into the optical computing chip.

6 . The gene alignment method of claim 1 , further comprising further obtaining the reference gene fragments from the gene database based on first m bases and last n bases of the to-be-tested gene sequence, wherein m and n are greater than 0, and wherein a sum of m and n is less than a quantity of bases in the to-be-tested gene sequence.

7 . A gene alignment apparatus comprising:

a processor configured to:

obtain reference gene fragments from a gene database based on a to-be-tested gene sequence, wherein the gene database comprises a reference gene sequence, wherein the reference gene sequence comprises the reference gene fragments, and wherein the reference gene fragments match some bases of the to-be-tested gene sequence;

determine, based on an output result of a first optical alignment, that a similarity degree between the to-be-tested gene sequence and a first gene fragment in the reference gene fragments is less than a first threshold and greater than a second threshold;

obtain a plurality of reference gene subsequences from the reference gene sequence, wherein the reference gene subsequences comprise a first reference gene subsequence;

make a determination that a first similarity degree is greater than a third threshold and less than a fourth threshold, wherein the fourth threshold is not greater than the first threshold; and

obtain, in response to the determination, a first to-be-tested gene subsequence and a second to-be-tested gene subsequence based on the to-be-tested gene sequence, wherein some bases of the first to-be-tested gene subsequence are the same as some bases of the second to-be-tested gene subsequence, and

an optical computing chip coupled to the processor and configured to:

input the to-be-tested gene sequence and the reference gene fragments;

perform the first optical alignment of the to-be-tested gene sequence and the reference gene fragments;

input the to-be-tested gene sequence and the first reference gene subsequence;

perform a second optical alignment of the to-be-tested gene sequence and the first reference gene subsequence to obtain the first similarity degree between the to-be-tested gene sequence and the first reference gene subsequence;

input the first to-be-tested gene subsequence and the first reference gene subsequence;

perform a third optical alignment of the first to-be-tested gene subsequence and the first reference gene subsequence to obtain a second similarity degree;

input the second to-be-tested gene subsequence and the first reference gene subsequence; and

perform a fourth optical alignment between the second to-be-tested gene subsequence and the first reference gene subsequence to obtain a third similarity degree.

8 . The gene alignment apparatus of claim 7 , wherein the processor is further configured to record, when the second similarity degree is greater than the fourth threshold, a location of the first reference gene subsequence in the reference gene sequence.

9 . The gene alignment apparatus of claim 7 , wherein the processor is further configured to obtain, when the third similarity degree is greater than the third threshold and less than the fourth threshold, a first to-be-tested gene subsequence unit and a second to-be-tested gene subsequence unit based on the second to-be-tested gene subsequence, wherein some bases of the first to-be-tested gene subsequence unit are the same as some bases of the second to-be-tested gene subsequence unit, and wherein the optical computing chip is further configured to:

input the first to-be-tested gene subsequence unit and the first reference gene subsequence;

perform a fifth optical alignment of the first to-be-tested gene subsequence unit and the first reference gene subsequence;

input the second to-be-tested gene subsequence unit and the first reference gene subsequence; and

perform a sixth optical alignment of the second to-be-tested gene subsequence unit and the first reference gene subsequence.

10 . The gene alignment apparatus of claim 7 , wherein the processor is further configured to:

determine, based on the output result, that a first reference gene fragment of the reference gene fragments matches the to-be-tested gene sequence; and

record a location of the first reference gene fragment in the reference gene sequence.

11 . The gene alignment apparatus of claim 7 , wherein the processor is further configured to separately perform optical encoding on the to-be-tested gene sequence and the reference gene fragments, and wherein the optical computing chip is further configured to separately input optical code of the to-be-tested gene sequence and optical code of the reference gene fragments.

12 . The gene alignment apparatus of claim 7 , wherein the processor is configured to further obtain the reference gene fragments from the gene database based on first m bases and last n bases of the to-be-tested gene sequence, wherein m and n are greater than 0, and wherein a sum of m and n is less than a quantity of bases in the to-be-tested gene sequence.

13 . An alignment apparatus comprising:

a processor configured to:

obtain a first group of reference objects from a database based on a first object, wherein at least some of the reference objects have some features that are the same as some features of the first object;

determine, based on an output result of a first optical alignment, that a similarity degree between the first object and a first reference object in the reference objects is less than a first threshold and greater than a second threshold;

obtain reference sub-objects based on a standard object, wherein each of the reference sub-objects is a part of one of the reference objects, and wherein the reference sub-objects comprise a first reference sub-object;

make a determination that a first similarity degree is greater than a third threshold and less than a fourth threshold, wherein the fourth threshold is not greater than the first threshold; and

obtain, in response to the determination, a first sub-object and a second sub-object based on the first object, wherein some data of the first sub-object is the same as some data of the second sub-object; and

an optical computing chip coupled to the processor and configured to:

perform the first optical alignment between the first object and the reference objects;

input the first object and the first reference sub-object;

perform a second optical alignment of the first object and the first reference sub-object to obtain the first similarity degree between the first object and the first reference sub-object;

input the first sub-object and the first reference sub-object;

perform a third optical alignment between the first sub-object and the first reference sub-object to obtain a second similarity degree;

input the second sub-object and the first reference sub-object; and

perform a fourth optical alignment between the second sub-object and the first reference sub-object to obtain a third similarity degree.

14 . The alignment apparatus of claim 13 , wherein the processor is further configured to record, when the second similarity degree is greater than the fourth threshold, a location of the first reference sub-object in the standard object.

15 . A non-transitory computer-readable storage medium comprising computer program instructions that, when executed by a processor, cause a gene alignment apparatus to:

obtain reference gene fragments from a gene database based on a to-be-tested gene sequence, wherein the gene database comprises a reference gene sequence, wherein the reference gene sequence comprises the reference gene fragments, and wherein the reference gene fragments match some bases of the to-be-tested gene sequence;

input the to-be-tested gene sequence and the reference gene fragments into an optical computing chip;

perform a first optical alignment of the to-be-tested gene sequence and the reference gene fragments using the optical computing chip;

determine, based on an output result of the first optical alignment, that a similarity degree between the to-be-tested gene sequence and a first gene fragment in the reference gene fragments is less than a first threshold and greater than a second threshold;

obtain a plurality of reference gene subsequences from the reference gene sequence, wherein the reference gene subsequences comprise a first reference gene subsequence;

input the to-be-tested gene sequence and the first reference gene subsequence into the optical computing chip;

perform a second optical alignment of the to-be-tested gene sequence and the first reference gene subsequence to obtain a first similarity degree between the to-be-tested gene sequence and the first reference gene subsequence;

make a determination that the first similarity degree is greater than a third threshold and less than a fourth threshold, wherein the fourth threshold is not greater than the first threshold;

obtain, in response to the determination, a first to-be-tested gene subsequence and a second to-be-tested gene subsequence based on the to-be-tested gene sequence, wherein some bases of the first to-be-tested gene subsequence are the same as some bases of the second to-be-tested gene subsequence;

input the first to-be-tested gene subsequence and the first reference gene subsequence into the optical computing chip;

perform a third optical alignment of the first to-be-tested gene subsequence and the first reference gene subsequence to obtain a second similarity degree;

input the second to-be-tested gene subsequence and the first reference gene subsequence into the optical computing chip; and

perform a fourth optical alignment of the second to-be-tested gene subsequence and the first reference gene subsequence to obtain a third similarity degree.

16 . The non-transitory computer-readable storage medium of claim 15 , wherein the computer program instructions, when executed by the processor further cause the gene alignment apparatus to record, when the second similarity degree is greater than the fourth threshold, a location of the first reference gene subsequence in the reference gene sequence.

17 . The non-transitory computer-readable storage medium of claim 15 , wherein the computer program instructions, when executed by the processor further cause the gene alignment apparatus to:

obtain, when the third similarity degree is greater than the third threshold and less than the fourth threshold, a first to-be-tested gene subsequence unit and a second to-be-tested gene subsequence unit based on the second to-be-tested gene subsequence, wherein some bases of the first to-be-tested gene subsequence unit are the same as some bases of the second to-be-tested gene subsequence unit;

input the first to-be-tested gene subsequence unit and the first reference gene subsequence;

perform a fifth optical alignment of the first to-be-tested gene subsequence unit and the first reference gene subsequence;

input the second to-be-tested gene subsequence unit and the first reference gene subsequence; and

perform a sixth optical alignment of the second to-be-tested gene subsequence unit and the first reference gene subsequence.

18 . The non-transitory computer-readable storage medium of claim 15 , wherein the computer program instructions, when executed by the processor further cause the gene alignment apparatus to:

determine, based on the output result, that a first reference gene fragment of the reference gene fragments matches the to-be-tested gene sequence; and

record a location of the first reference gene fragment in the reference gene sequence.

19 . The non-transitory computer-readable storage medium of claim 15 , wherein the computer program instructions, when executed by the processor further cause the gene alignment apparatus to separately perform optical encoding on the to-be-tested gene sequence and the reference gene fragments, and wherein the optical computing chip is further configured to separately input optical code of the to-be-tested gene sequence and optical code of the reference gene fragments.

20 . The non-transitory computer-readable storage medium of claim 15 , wherein the computer program instructions, when executed by the processor further cause the gene alignment apparatus to further obtain the reference gene fragments from the gene database based on first m bases and last n bases of the to-be-tested gene sequence, wherein m and n are greater than 0, and wherein a sum of m and n is less than a quantity of bases in the to-be-tested gene sequence.

21 . An alignment method implemented by a computer system comprising an optical computing chip, the alignment method comprising:

obtaining a first group of reference objects from a database based on a first object, wherein at least some of the reference objects have some features that are the same as some features of the first object;

determining, based on an output result of a first optical alignment, that a similarity degree between the first object and a first reference object in the reference objects is less than a first threshold and greater than a second threshold;

obtaining reference sub-objects based on a standard object, wherein each of the reference sub-objects is a part of one of the reference objects, and wherein the reference sub-objects comprise a first reference sub-object;

making a determination that a first similarity degree between the first object and the first reference sub-object is greater than a third threshold and less than a fourth threshold, wherein the fourth threshold is not greater than the first threshold;

obtaining, in response to the determination, a first sub-object and a second sub-object based on the first object, wherein some data of the first sub-object is the same as some data of the second sub-object;

performing the first optical alignment between the first object and the reference objects;

inputting the first object and the first reference sub-object into the optical computing chip;

performing a second optical alignment of the first object and the first reference sub-object to obtain the first similarity degree;

inputting the first sub-object and the first reference sub-object into the optical computing chip;

performing a third optical alignment between the first sub-object and the first reference sub-object to obtain a second similarity degree;

inputting the second sub-object and the first reference sub-object into the optical computing chip; and

performing a fourth optical alignment between the second sub-object and the first reference sub-object to obtain a third similarity degree.

22 . The alignment method of claim 21 , further comprising recording, when the second similarity degree is greater than the fourth threshold, a location of the first reference sub-object in the standard object.