Sequence Alignment Compression Using Consensus Pointer Pairs

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Solution Overview

Problem

Existing data compression methods are inefficient in reducing storage and bandwidth requirements, particularly for large files, due to inadequate utilization of sequence alignment techniques.

Innovation Solution

A compression engine that splits files into sequences, aligns them using a consensus matrix, and represents the original file as a list of pointer pairs to a consensus sequence, allowing for efficient compression and reconstruction.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Quantity of substance

If traditional compression methods are used, then storage space and bandwidth are reduced, but compression efficiency is insufficient for large files

Engineering Contradiction:

Improvestorage spaceVSAvoidcompression efficiency

Core Design Contradiction:

Quantity of substanceVSProductivity

Solution Approach 1:

The input file is divided into multiple sequences of equal length, which are then processed independently through alignment operations. This segmentation allows the compression algorithm to work on smaller manageable units, improving overall compression efficiency while achieving better storage reduction

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

A consensus sequence is introduced as an intermediary representation that captures the common patterns across multiple input sequences. Instead of compressing each sequence individually, the system creates a shared consensus sequence that represents the majority pattern, significantly reducing storage requirements while maintaining compression quality

Inventive Principle:

Principle #24Intermediary (Mediator)

2Quantity of substance

If sequence alignment techniques are applied, then compression ratio improves, but computational complexity increases

Engineering Contradiction:

Improvecompression ratioVSAvoidcomputational complexity

Core Design Contradiction:

Quantity of substanceVSDevice complexity

Solution Approach 1:

By dividing the file into smaller sequences of equal length, the alignment operations can be performed on manageable units rather than the entire file at once. This reduces the computational burden of each alignment operation while achieving better overall compression ratios through the cumulative effect of aligning multiple segments

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The system transforms the input sequences into a consensus sequence by identifying and aligning common patterns. This parameter transformation converts complex variable-length sequences into a standardized format that is easier to process and store, improving compression ratio while controlling computational complexity through systematic parameter changes

Inventive Principle:

Principle #35Parameter changes

Data Source

PatentUS12530320B2File compression using sequence splits and sequence alignment

Publication Date: 2026.01.20 DELL PROD LP

AI summary

Compressing files is disclosed. An input file to be compressed is first aligned. Aligning the file includes splitting the file into sequences that can be aligned. When splitting the file into sequences or when performing subsequent recursive splitting, the splitting is based on a longest sequence match. The result is a compression matrix, where each row of the matrix corresponds to part of the file. A consensus sequence is determined from the compression matrix. Using the consensus sequence, pointer pairs are generated. Each pointer pair identifies a subsequence of the consensus matrix. The compressed file includes the pointer pairs and the consensus sequence.