Multivalent ISV Sequence Assembly Using Candidate Read Matching
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Solution Overview
Problem
Obtaining sequence information for multivalent immunoglobulin single variable domains (ISVs) is challenging due to the large size of the sequences and the complexity of repetitive sequences, making conventional sequencing techniques inefficient and time-consuming.
Innovation Solution
A computer-implemented method that receives sequence information for component ISVs, generates candidate sequences, determines hit candidate sequences through pattern matching, and constructs consensus and assembly matrices to rapidly determine sequence information for each target multivalent ISV, ensuring high accuracy and efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional sequencing techniques are used to sequence multivalent ISV fragments, then sequence information can be obtained, but the process is time-consuming and difficult due to large sequence size and repetitive sequences
Solution Approach 1:
The patent segments the multivalent ISV sequencing problem into multiple independent fragment sequences, each processed separately through pattern matching against candidate sequences. This allows parallel processing of multiple fragments simultaneously, dramatically reducing total sequencing time while maintaining accuracy through individual fragment analysis
Solution Approach 2:
The patent performs preliminary generation of candidate multivalent ISV sequences from component ISV sequences before actual sequencing occurs. This pre-computation creates a reference database that enables rapid pattern matching during sequencing, eliminating the need for time-consuming de novo assembly of repetitive sequences
2Measurement precision
If conventional sequencing techniques are used to sequence multivalent ISV fragments, then sequence information can be obtained, but the process is difficult due to repetitive sequences requiring joining together
Solution Approach 1:
The patent creates copies of component ISV sequences to generate multiple candidate multivalent ISV sequences. These candidate sequences serve as templates for pattern matching, allowing the system to identify and validate sequence fragments without complex assembly operations. The copying approach simplifies the process by replacing difficult joining operations with straightforward pattern comparison
Solution Approach 2:
The patent implements feedback through pattern matching, where each sequenced fragment is compared against the pre-generated candidate sequences. The matching results provide immediate validation and identification information, eliminating the need for complex iterative assembly processes. The feedback mechanism confirms sequence identity through direct comparison rather than indirect assembly inference
3Productivity
If rapid determination of sequence information is achieved through automated methods, then productivity increases, but measurement precision may be compromised
Solution Approach 1:
The patent performs preliminary generation of all possible candidate multivalent ISV sequences from component ISVs before sequencing. This pre-computation creates a complete reference database that enables rapid and unambiguous pattern matching during sequencing. The preliminary action eliminates computational ambiguity during the actual sequencing process, ensuring high accuracy while enabling rapid processing
Solution Approach 2:
The patent generates multiple copies of component sequences to create candidate multivalent ISV sequences. These copies serve as reference templates for pattern matching, allowing rapid identification of actual sequences through direct comparison. The copying approach enables parallel processing of multiple candidates simultaneously, increasing throughput while maintaining precision through exact sequence matching
Data Source
AI summary
A computer-implemented method for obtaining sequence information for each of a plurality of target multivalent immunoglobulin single variable domains (ISVs) comprises: receiving sequence information for component ISVs; generating candidate sequences of multivalent ISVs based on the received sequence information; obtaining groups of reads of sequencing information corresponding to target multivalent ISVs; for each read: determining hit candidate sequences from the set of candidate sequences and generating consensus matrices for hit candidate sequences; generating, for each group of reads, an assembly matrix for each hit candidate sequence; and determining sequence information for each target multivalent ISV.