Codon Inverted Indexing for Fast Segmented Genome Mutation Analysis
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Solution Overview
Problem
The analysis of personal genomes is hindered by large data sizes and lengthy processing times due to segmented base sequences, which are conventionally connected using methods like Burrows-Wheeler transform, leading to inefficient analysis.
Innovation Solution
An information processing apparatus encodes base sequences into codon units using a codon conversion table and generates bitmap-type inverted indexes to facilitate rapid analysis of gene mutations without connecting segmented data, utilizing codon conversion and inverted indexing techniques to speed up the analysis of gene mutations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If segmented base sequences are connected using conventional methods (Burrows-Wheeler transform, block sorting), then the base sequence can be assembled into a complete genome, but the analysis time becomes significantly long
Solution Approach 1:
The patent maintains segmented base sequences without connecting them into a complete genome. Instead of assembling the full genome which would take significant time, the system analyzes each segment independently using codon-based inversion indexing, thereby reducing analysis time while still achieving reliable mutation detection across the entire genome through aggregation of segment results
Solution Approach 2:
The patent introduces an intermediary representation called the inverted index of codon sequences. This intermediary structure allows the system to search and compare genetic segments efficiently without actually assembling the complete genome sequence. The inverted index maps codon sequences to their positions in segmented data, enabling rapid retrieval and comparison operations that would be computationally intensive if performed on the full assembled genome
2Reliability
If segmented base sequences are connected to form complete genome data, then the genome can be analyzed comprehensively, but the data size after connection becomes large
Solution Approach 1:
The patent extracts only the necessary information for mutation detection by creating an inverted index of codon sequences from the segmented base sequences. This extraction process removes redundant information and retains only the essential codon-based positional mappings, significantly reducing the data size required for comprehensive genome analysis while maintaining analysis comprehensiveness through the index structure
Solution Approach 2:
The patent transforms the data representation from a one-dimensional sequence format to a two-dimensional inverted index structure. The inverted index organizes codon sequences by their positions in the segmented data, creating a dimensional transformation that enables comprehensive search and comparison operations with reduced data volume. This dimensional change allows the system to access any segment quickly without storing the entire assembled genome
3Reliability
If conventional connection methods are used for segmented base sequences, then the genome can be assembled, but the processing speed becomes slow
Solution Approach 1:
The patent performs preliminary action by pre-computing the inverted index of codon sequences from the segmented base sequences before actual analysis begins. This preliminary indexing process organizes the data in advance, allowing subsequent mutation detection and comparison operations to proceed at high speed through direct index lookup rather than sequential scanning or assembly operations, thereby significantly improving processing speed
Solution Approach 2:
The patent replaces the mechanical assembly process (conventional connection methods like Burrows-Wheeler transform) with a computational indexing approach. Instead of physically assembling the complete genome sequence through complex sorting and merging operations, the system uses the inverted index structure to directly access and compare codon sequences, substituting the mechanical assembly process with a more efficient computational search mechanism that dramatically improves processing speed
Data Source
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AI summary
An information processing apparatus is configured to: obtain pieces of segmented genome data being genome information of a specific individual; generate pieces of segmented codon data obtained by encoding each of the pieces of segmented genome data in a codon unit based on a table in which a codon is associated with a code; identify, based on reference codon data obtained by encoding reference genome data to be a reference in the codon unit and each of the pieces of segmented codon data, a type and a position of an appearance of gene mutation different from the code in the reference codon data among the codes in the pieces of segmented codon data; and generate a gene mutation inverted index in which the gene mutation and the type and position of the appearance of the gene mutation are associated with each other.