ARTS

ARTS performs three-dimensional structural alignment and retrieval of common substructures in nucleic acids (RNA and DNA) to enable comparative structural analysis and identification of SNP-based genomic markers.

Key Features:

• 3D Structural Alignment: Aligns tertiary structures of nucleic acids in three dimensions, enabling comparison of global folds and local motifs.
• Detection of Common Substructures: Identifies common substructures ranging from large folds involving hundreds to thousands of nucleotides to small motifs with at least two successive base pairs.
• Sequence-order-independent Alignment: Searches for common substructures without relying on nucleotide sequence order, using spatial configuration as the basis for alignment.
• Scalability and Large-scale Comparison: Demonstrated efficiency for comprehensive all-against-all comparisons within large databases such as the Protein Data Bank (PDB).
• SNP Retrieval and Marker Design: Retrieves single nucleotide polymorphisms (SNPs) polymorphic between mouse strains and has been applied to design genome-wide SNP marker panels.

Scientific Applications:

• RNA Structural Analysis: Aligns RNA structures to reveal shared structural features relevant to RNA function.
• Non-Coding RNA Research: Enables tertiary-structure-based analysis of non-coding RNAs where protein-structure approaches are more developed.
• Genomic Marker Design: Supports identification of polymorphic SNPs across strains for genome-wide marker panel development.

Methodology:

ARTS receives pairs of 3D nucleic acid structures and searches for a priori unknown common substructures; the alignment process is independent of nucleotide sequence order and focuses on spatial configuration; validation includes extensive all-against-all comparisons within the PDB.