OLIGOMER SEQUENCES MAPPING

• US 20110015864A1
• Filed: 02/02/2010
• Published: 01/20/2011
• Est. Priority Date: 02/03/2009
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Halpern, Aaron L., Nazarenko, Igor
• Granted Patent: US 8,731,843 B2
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.

Claims

1. A method of oligomer sequence mapping, comprising:

a. receiving a data set of related oligomer sequences;

b. applying one or more key patterns to the oligomer sequences in the data set to generate one or more keys comprising selected positions of the oligomer sequences;

c. modifying one or more positions to create a set of modified keys; and

d. comparing the modified keys to a reference index to determine candidate locations of the oligomer sequences in the reference.

2. The method of claim 1, wherein the positions are modified in the data set prior to application of the key pattern.

3. The method of claim 1, wherein the positions are modified following application of the key pattern.

4. The method of claim 1, further comprising:

e. validating candidate locations by comparing all bases of a dataset to the indicated portions of the reference.

5. The method of claim 1, wherein the modifications are base substitutions to reflect all possible bases or combinations of bases at the modified positions.

6. The method of claim 1, wherein the majority or all of the individual positions in a key or data set are individually substituted to create the set of modified keys.

7. The method of claim 6, wherein the substitutions are adjacent substitutions.

8. The method of claim 6, wherein the substitutions are overlapping substitutions.

9. The method of claim 6, wherein the substitutions are non-adjacent substitutions.

10. The method of claim 1, wherein the modifications are additions or deletion of positions in a key.

11. The method of claim 10, wherein the positions are modified individually.

12. The method of claim 1, wherein the keys are reordered.

13. A method of oligomer sequence mapping, comprising:

a. receiving a data set of related oligomer sequences;

b. applying one or more key patterns to the oligomer sequences in the data set to generate one or more keys;

c. modifying individual positions to create a first set of modified keys;

d. modifying two or more combined positions to create a second set of modified keys; and

e. comparing the first and second set of modified keys to a reference index to determine candidate locations of the oligomer sequences in the reference.

14. The method of claim 13, further comprising:

f. validating candidate locations by comparing all bases of a dataset to the indicated portions of the reference

15. The method of claim 13, wherein the modifications of the individual positions reflect all possible bases or combinations thereof.

16. A method of oligomer sequence mapping, comprising:

a. receiving a data set of related oligomer sequences;

b. applying one or more key patterns to the oligomer sequences in the data set to generate one or more keys;

c. modifying two or more combined positions to create a first set of modified keys;

d. modifying two or more combined positions to create a second set of modified keys; and

e. comparing the first and second set of modified keys to a reference index to determine candidate locations of the oligomer sequences in the reference.

17. The method of claim 16, further comprising:

f. validating candidate locations by comparing all bases of a dataset to the indicated portions of the reference.

18. An oligomer sequence mapping system comprising:

a. an interface configured to receive a data set of related oligomer sequences; and

b. a processor coupled to the interface, wherein the processor is configured to;

apply one or more key patterns to information in the data set to generate one or more keys from the data set, modify the majority or all of the positions within the key to create a set of modified keys, and

compare the keys generated from the data set and the modified keys to a reference index to determine candidate locations of the oligomer sequences in the reference.

19. The system of claim 18, wherein the processor is further configured to validate the candidate locations.

20. The system of claim 18, wherein the processor is further configured to output locations of the oligomer sequences in the reference.

21. The system of claim 18, wherein the processor is configured to perform multiple modification regimes using a single oligomer data set.

22. The product of claim 18, wherein individual positions are modified.

23. The product of claim 18, wherein two or more combined positions are modified.

24. The system of claim 19, wherein the processor is configured to apply one or more key patterns to information in the data set to generate one or more keys from the data set, and to substitute the majority or all of the positions to create a set of modified keys to reflect all possibilities of bases or combinations thereof.

25. A computer program product for oligomer sequence mapping, the computer program product being embodied in a computer readable medium and comprising computer instructions for:

a. receiving a data set of related oligomer sequences;

b. applying one or more key patterns to information in the data set to generate one or more keys;

c. modifying multiple positions within the keys to create a set of modified keys; and

d. comparing the modified keys to a reference index to determine candidate locations of the oligomer sequences in the reference.