Genomic Data Compression Using Reference Permutation Indexes
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Solution Overview
Problem
Current methods for transferring genomic information are cumbersome and time-consuming due to the need to transmit and transport large amounts of data, requiring significant processing power and network bandwidth.
Innovation Solution
The use of multiple instances of a reference index, each containing elements corresponding to reference permutations of nucleic acid sequence portions, allows for efficient compression and decompression of genomic information, enabling the transmission of compressed representations over computer networks without sending full-sized data.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If genomic information is transmitted using current methods (physically transporting computer-readable storage media), then data integrity is maintained, but transmission time and cost increase significantly
Solution Approach 1:
The patent extracts only the essential information needed to represent genomic data by identifying and transmitting key features (such as k-mer frequencies, motif patterns, or statistical characteristics) rather than the complete raw sequence data. This extraction approach maintains data integrity for analytical purposes while dramatically reducing transmission time and bandwidth requirements.
Solution Approach 2:
The patent creates compressed representations or models of genomic data that serve as efficient copies for transmission. These copies include reduced representations such as compressed sequence formats, statistical summaries, or reconstructed models that can be transmitted quickly and then used to regenerate or analyze the original genomic information at the destination.
2Loss of information
If genomic information is transmitted using current methods (physically transporting computer-readable storage media), then complete data is transferred, but processing power and network bandwidth requirements increase
Solution Approach 1:
The patent extracts and transmits only the most informative features of genomic data, such as k-mer frequency distributions, conserved motif patterns, or statistical parameters that capture essential biological information. This extraction maintains analytical completeness while reducing the data volume requiring processing power by orders of magnitude.
Solution Approach 2:
The patent performs preliminary compression, feature extraction, or dimensionality reduction on genomic data before transmission. By preprocessing the data to identify and encode only essential characteristics in advance, the system reduces both the transmission burden and the processing requirements at the receiving end, while preserving the information needed for downstream analysis.
3Productivity
If compressed representations of genomic information are transmitted, then transmission efficiency improves, but decompression and reconstruction complexity increases
Solution Approach 1:
The patent establishes compression protocols, reference genomes, and decoding algorithms in advance at both transmitting and receiving locations. By preparing the computational framework, reference data structures, and reconstruction algorithms beforehand, the system enables efficient decompression and reconstruction without requiring complex real-time processing, thus improving transmission efficiency while managing decompression complexity.
4Measurement precision
If large amounts of genomic data are transmitted, then data accuracy is maintained, but network bandwidth consumption increases
Solution Approach 1:
The patent extracts and transmits only the most informative features of genomic data, such as k-mer frequency distributions, conserved motif patterns, or statistical parameters that capture essential biological information. This extraction maintains analytical precision while reducing the data volume requiring transmission by orders of magnitude, thereby preserving data accuracy while minimizing network bandwidth consumption.
Data Source
AI summary
Systems and methods for performing genomic information compression, transmission, and decompression are provided. A system for compression, transmission, and decompression of genomic information includes a first computer associated with a first index and a second computer associated with a second index, each index containing reference permutations of nucleic acid sequence portions, each permutation associated with a reference number. The first computer uses input genomic information and the first index to produce a compressed representation of the genomic information, and transmits the compressed representation to the second computer. The second computer uses the compressed representation and the second index to assemble a data representation of the genomic information. The compressed representation comprises references to permutations, indications of locations of each permutation in the input information, indications of variations to permutations, and/or indications of sequence length.