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US 2008/0189049 A1Published application
System and methods for indel identification using short read sequencing
AssigneeApplera Corporation
InventorZheng ZHANG
Life of this patent
Estimating the term…
Abstract
Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.
Claims20
A method of nucleic acid sequence analysis, comprising:
- receiving nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise non-overlapping pairwise sequences separated by an intervening sequence length;
- receiving nucleic acid sequence information comprising at least one reference sequence;
- performing a mapping operation for each of the one or more mate pair sequences in which the non-overlapping pairwise sequences are aligned to the at least one reference sequence by the steps of:
- performing a first mapping operation aligning the non-overlapping pairwise sequences to the at least one reference sequence with a selected mismatch constraint identifying non-overlapping pairwise sequences for which one of the non-overlapping pairwise sequences align to the at least one reference sequence while satisfying the selected mismatch constraint;
- performing a second mapping operation designating a window region of the reference sequence to align the non aligned pairwise sequence with a selected mismatch constraint;
- identifying non-overlapping pairwise sequences that are successfully mapped following performing the first and second mapping operations;
- and,
- outputting the results of the mapping operations.
5 more elements
A system for nucleic acid sequence analysis, comprising:
- a data analysis unit configured to:
- receive nucleic acid sequence information for one or more mate pair sequences, wherein mate pair sequences comprise non-overlapping pairwise sequences separated by an intervening sequence length and further configured to receive nucleic acid sequence information for at least one reference sequence;
- perform a mapping operation for each of the one or more mate pair sequences in which the non-overlapping pairwise sequences are aligned to the at least one reference sequence by the steps of:
- performing a first mapping operation aligning the non-overlapping pairwise sequences to the at least one reference sequence with a selected mismatch constraint identifying non-overlapping pairwise sequences for which one of the non-overlapping pairwise sequences align to the at least one reference sequence while satisfying the selected mismatch constraint;
- performing a second mapping operation designating a window region of the reference sequence to align the non aligned pairwise sequence with a selected mismatch constraint;
- identify non-overlapping pairwise sequences that are successfully mapped following performing the first and second mapping operations;
- and,
- a data terminal for displaying the results of the mapping operations generated by the data analysis unit to a user.
5 more elements
A computer-readable medium, the computer-readable medium being readable to execute a method of nucleic acid sequence analysis, the method comprising:
- receiving nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise non-overlapping pairwise sequences separated by an intervening sequence length;
- receiving nucleic acid sequence information comprising at least one reference sequence;
- performing a mapping operation for each of the one or more mate pair sequences in which the non-overlapping pairwise sequences are aligned to the at least one reference sequence by the steps of:
- performing a first mapping operation aligning the non-overlapping pairwise sequences to the at least one reference sequence with a selected mismatch constraint identifying non-overlapping pairwise sequences for which one of the non-overlapping pairwise sequences align to the at least one reference sequence while satisfying the selected mismatch constraint;
- performing a second mapping operation designating a window region of the reference sequence to align the non aligned pairwise sequence with a selected mismatch constraint;
- identifying non-overlapping pairwise sequences that are successfully mapped following performing the first and second mapping operations;
- and,
- outputting the results of the mapping operations.
5 more elements
Dependencies are inferred from the claim text.