NeSSie

NeSSie identifies and analyzes approximate symmetrical patterns in DNA sequences to detect non-B DNA conformations such as palindromes, mirrors, hairpins, cruciforms, and triplex-forming motifs.

Key Features:

• Comprehensive symmetry detection: Performs genome-wide searches for exact and degenerate symmetrical patterns including perfect DNA palindromes, mirror sequences, hairpins, cruciforms, and triplex-forming patterns.
• Dynamic programming algorithm: Uses dynamic programming to efficiently scan large genomic datasets and identify symmetrical motifs.
• Implementation in C/C++ 64-bit: Provided as a C/C++ 64-bit library and tool, allowing customization for specific research needs.
• Linguistic complexity and Shannon entropy analysis: Computes linguistic complexity and Shannon entropy measures to assess the repetitiveness of DNA regions enriched for identified motifs.

Scientific Applications:

• Non-B DNA structure analysis: Identification of regions that can form non-B DNA conformations to study their roles in genomic rearrangements and structural organization.
• Gene regulation and genomic stability: Enables investigation of potential associations between symmetrical motifs and gene expression regulation or genomic instability.
• Microbial genomics case study: Demonstrated utility through analysis of the Mycobacterium bovis genome.

Methodology:

NeSSie employs a dynamic programming approach to scan entire genomes for perfect and degenerate symmetrical DNA motifs and computes linguistic complexity and Shannon entropy for identified regions.