DNA Sequence Assembly Using Anchor Sequences
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Solution Overview
Problem
Current DNA sequencing technologies break large DNA fragments into small pieces for sequencing, leading to complex assembly challenges due to redundant and overlapping fragments with errors, making it difficult to reconstruct the original large DNA sequence accurately.
Innovation Solution
A method using a computer system to index, group, and consolidate DNA fragment reads based on anchor and shoulder sequences, elongating reads to increase average length, preserve Indels and SNPs, and reduce low-frequency errors, thereby improving the assembly of contiguous DNA segments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If DNA fragments are broken into small pieces for sequencing, then sequencing capability is improved, but assembly complexity increases
Solution Approach 1:
The patent applies segmentation by dividing the assembly process into distinct stages: indexing fragment reads using anchor sequences (specific 12-mer sequences), grouping reads by anchor matches, and then assembling within groups. This segmented approach manages the complexity of assembling small DNA fragments by breaking down the overall assembly task into smaller, more manageable sub-tasks.
Solution Approach 2:
The patent introduces anchor sequences as intermediary elements to facilitate assembly. These specific 12-mer sequences serve as mediators that link overlapping fragment reads together. By using anchor sequences as intermediaries, the system can systematically connect small DNA fragments without requiring complex global optimization algorithms.
2Reliability
If redundant overlapping fragments are used to maximize coverage, then sequencing accuracy is improved, but assembly difficulty increases
Solution Approach 1:
The patent applies preliminary action by pre-indexing fragment reads based on their anchor sequence content before the actual assembly process. This pre-processing step organizes the redundant overlapping fragments into groups that share common anchor sequences, making the subsequent assembly task more tractable despite the redundancy.
Solution Approach 2:
The patent changes parameters by focusing assembly efforts on specific anchor sequences (12-mers) rather than considering all possible overlaps. This parameter change transforms the assembly problem from a global optimization challenge into a series of localized assembly tasks centered around anchor matches, reducing overall complexity.
3Productivity
If short reads are used to increase throughput, then sequencing speed is improved, but assembly precision deteriorates
Solution Approach 1:
The patent applies merging by consolidating multiple short fragment reads that share common anchor sequences into longer contiguous sequences. By merging overlapping reads around anchor points, the system recovers length information that was lost in the short read sequencing process, thereby improving assembly precision while maintaining the high throughput benefits of short read technology.
Data Source
AI summary
Certain embodiments of the invention provide systems and methods for the automated assembly of DNA sequence data into contiguous DNA segments using a computer a system. DNA sequence data is entered into the system. The system indexes and groups a plurality of DNA fragment reads utilizing an anchor sequence and consolidates the fragments into larger sequences by merging the fragment reads within a group.