Protein Primary Structure Identification via Codon Indexing
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Solution Overview
Problem
Conventional technologies fail to efficiently identify the primary structure of proteins within genomes due to the inability to convert amino acid information into codon information, leading to reduced speed in identifying primary structures due to the large amount of dictionary information required for comparison.
Innovation Solution
A method involving the generation of a codon compression file and codon transposition index from a base file using a conversion table, followed by the creation of a protein hidden Markov model and dictionary index to identify protein codes and calculate cooccurrence rates, allowing for the identification of primary structures by cutting out codon code sequences in units of correct proteins.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional base or amino acid sequence comparison is used to search genomes, then the search can be performed, but the identification speed is reduced due to the large amount of dictionary information required for comparison
Solution Approach 1:
The invention segments the genome search process by dividing base sequences into codon units (groups of three bases) and creating separate index structures for codons and amino acids. This segmentation allows the system to avoid comparing against entire amino acid dictionaries, instead using smaller codon-based indexes that significantly reduce the amount of dictionary information needed while maintaining identification accuracy.
Solution Approach 2:
The invention introduces codon information as an intermediary between base sequences and amino acids. By creating codon indexes and using codon-amino acid correspondence tables, the system mediates the search process, allowing efficient base sequence comparison through codon units rather than requiring direct comparison with large amino acid dictionaries, thus improving speed while reducing dictionary information requirements.
2Productivity
If amino acid information is used to identify primary structures, then the identification can be performed, but the speed is reduced due to inability to convert amino acid information into codon information
Solution Approach 1:
The invention performs preliminary action by pre-converting base sequences into codon units and creating codon indexes before the actual search process. By organizing the data structure in advance with codon-amino acid correspondence tables and codon-based indexes, the system eliminates the need for real-time conversion during identification, significantly improving processing speed while maintaining the ability to accurately identify primary structures.
3Quantity of substance
If base files are encoded in units of proteins, then compression rates increase, but the complexity of encoding and decoding processes increases
Solution Approach 1:
The invention segments the encoding process into distinct stages: base-to-codon conversion, codon-to-amino acid mapping, and protein-level compression. By creating separate index structures for codons and amino acids, and using systematic numbering schemes, the system achieves effective protein-unit compression while managing complexity through modular, staged processing rather than monolithic encoding.
Data Source
AI summary
An identification apparatus acquires a protein file in which a plurality of proteins including a plurality of amino acids are arranged. The identification apparatus identifies a plurality of primary structure candidates with any position included in the protein file as a starting position. The identification apparatus identifies one primary structure among the primary structure candidates based on a combination of a primary structure and each amino acid and a primary structure table, where the each amino acid is positioned at an end of the primary structure and the primary structure table associates a primary structure and a cooccurrence rate of a certain amino acid combination positioned at an end of the primary structure.