Structured ASIC Genomic Pipeline for Fast Sequence Alignment
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Solution Overview
Problem
Current bioinformatics methods for analyzing genomic data are labor-intensive, time-consuming, and prone to errors, particularly in assembling full-length genomic sequences and determining variants, due to the large volume of DNA sequence fragments that need to be mapped, aligned, and compared to a reference genome.
Innovation Solution
Implementing bioinformatics protocols on an integrated circuit processing platform using hardwired digital logic circuits interconnected by physical electrical interconnects, forming processing engines capable of performing tasks such as mapping, alignment, and sorting of genetic data, thereby optimizing the analysis pipeline for faster and more accurate results.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional software-based bioinformatics methods are used to map, align, and compare DNA sequence fragments, then the analysis can be performed with flexibility and adaptability, but the process becomes labor-intensive, time-consuming, and prone to errors
Solution Approach 1:
The patent replaces software-based mechanical processing with hardware-based electronic processing. Digital logic circuits perform mapping, aligning, and comparing operations in parallel, transforming the mechanical sequence of operations into simultaneous electronic computations that occur at the speed of electrical signals rather than software execution cycles
Solution Approach 2:
The patent divides the genomic data processing into multiple parallel processing paths within the digital logic circuit. Different segments of DNA sequence fragments are processed simultaneously by separate logic circuit units, each handling specific mapping, aligning, or comparing tasks, thereby achieving parallel processing that dramatically reduces overall analysis time
2Reliability
If manual or software-based methods are used to assemble full-length genomic sequences from fragments, then the process can be performed with standard tools, but it requires significant labor and is prone to errors
Solution Approach 1:
The patent replaces manual and software-based assembly operations with automated digital logic circuit operations. The hardware systematically performs fragment matching, gap filling, and sequence verification through dedicated logic units that eliminate human error and provide consistent, reproducible results
Solution Approach 2:
The digital logic circuit is designed to automatically perform the complete assembly process without external intervention. The circuit self-corrects errors through built-in verification logic and automatically assembles fragments based on complementary base pairing rules, reducing the system to self-service operation
3Quantity of substance
If large volumes of DNA sequence fragments are processed using conventional methods, then comprehensive analysis can be achieved, but the data analysis bottleneck prevents faster processing
Solution Approach 1:
The patent segments the large volume of DNA sequence data into multiple parallel processing streams that can be handled simultaneously by the digital logic circuit. Each stream is processed independently through dedicated logic units, allowing the system to handle comprehensive data volumes while maintaining high processing throughput through parallelization
Solution Approach 2:
The patent transitions from sequential one-dimensional processing to multi-dimensional parallel processing. The digital logic circuit processes multiple fragments, sequences, and comparisons simultaneously across multiple logical dimensions, effectively adding a parallelism dimension that resolves the bottleneck between data volume and processing speed
Data Source
AI summary
A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.