Gene Assembly Error Correction Using High Frequency Short String Detection
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Solution Overview
Problem
Existing gene sequencing technologies face errors in base sequencing, leading to low utilization of test sequences due to ineffective error correction strategies that fail to address the issue of low frequency short strings, resulting in suboptimal data analysis and assembly.
Innovation Solution
A computer-implemented method and system that identify high frequency short strings, search for continuous areas with the largest number of these strings, and recombine them into continuous sequences using left and right side trees, improving sequence utilization by retaining the original sequence's length and number.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If low frequency short strings are screened out and deleted from test sequences, then sequencing errors are reduced, but test sequence utilization becomes low
Solution Approach 1:
The patent changes the frequency threshold parameter dynamically. Instead of uniformly deleting all low frequency short strings, it sets different frequency thresholds for different positions in the test sequence. High frequency threshold is applied at sequence ends where errors are more likely, while lower threshold is applied in middle regions to preserve valid sequences, thus improving error correction while maintaining sequence utilization
Solution Approach 2:
The patent applies different error correction strategies to different parts of the test sequence. The frequency threshold for identifying short strings is adjusted locally based on position: stricter filtering at sequence ends and more lenient filtering in middle regions. This localized approach corrects errors where they occur most while preserving valid sequences in less error-prone regions
2Device complexity
If simple screening of low frequency short strings is performed, then error correction is simplified, but effective error correction is not achieved
Solution Approach 1:
The patent performs preliminary classification of short strings by frequency before the main error correction process. It first identifies high frequency and low frequency short strings separately, then applies different handling strategies to each category. This preliminary action enables more effective error correction by distinguishing between likely errors (low frequency) and valid sequences (high frequency) before the main correction logic is applied
3Measurement precision
If deep sequencing depth is used, then sequencing accuracy is improved, but the probability of errorless sequences containing low frequency short strings becomes very low
Solution Approach 1:
The patent uses feedback from the frequency analysis to dynamically adjust the correction strategy. By counting the frequency of each short string and comparing it against position-dependent thresholds, the system receives feedback about whether a short string is likely an error or valid. This feedback mechanism allows the system to correct errors while preserving valid low frequency sequences that pass the frequency threshold test
Data Source
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AI summary
The present invention provides an error correcting method of test sequence, which involves receiving test sequences, configuring high frequency short string list based on a preset high frequency threshold value, traversing each received test sequence, searching an area with the largest number of continuous high frequency short strings on each test sequence in combination with high frequency short string list, configuring whole left sequence and/or right sequence of high frequency short strings at left side and/or right side of searched area according to corresponding received test sequence and high frequency short string list, and constituting corresponding test sequence according to configured left and/or right sequence and searched area. The present invention also provides corresponding error correcting system of test sequence and gene assembly equipment.