GenCompress

GenCompress compresses DNA sequences losslessly by identifying and exploiting approximate repeats to reduce storage requirements and support analyses of sequence relatedness.

Key Features:

• Lossless compression: Preserves all nucleotide information while reducing DNA sequence size.
• Approximate repeat detection: Systematically searches for patterns that recur with slight variations across sequences.
• Redundancy exploitation: Exploits subtle sequence redundancies to achieve improved compression.
• Benchmark performance: Demonstrates superior compression ratios on benchmark DNA sequences compared with existing methods.
• Sequence relatedness metric: Implements a theoretical framework that measures relatedness between two DNA sequences.
• Experimental validation: Algorithm behavior and the theoretical framework have been validated through experiments on DNA sequence datasets.

Scientific Applications:

• Comparative genomics: Enables efficient storage and comparison of genomes across species or within populations.
• Phylogenetics: Assists in constructing evolutionary trees and analyzing evolutionary relationships.
• Genomic data management: Reduces storage and retrieval burden for large genomic datasets.

Methodology:

Systematic search for approximate repeats and exploitation of these subtle redundancies to perform lossless compression; application of a theoretical framework to measure relatedness between two DNA sequences; experimental validation on benchmark DNA sequences.