DiProGB

DiProGB encodes nucleotide sequences into physico-chemical dinucleotide property-based sequence graphs to visualize and analyze DNA and RNA thermodynamic and geometrical features such as stacking energy, melting temperature, and twist angle.

Key Features:

• Visualization: Converts primary nucleotide sequences into sequence graphs that represent thermodynamical and geometrical dinucleotide properties including stacking energy, melting temperature, and twist angle.
• Graph Manipulation: Enables manipulation and exploration of sequence graphs to inspect encoded physico-chemical signals.
• Conservation Analysis: Identifies regions where physico-chemical properties are more conserved than nucleotide sequences, indicating potential structural conservation.
• Data Modes: Supports analysis of both primary nucleotide sequences and their corresponding encoded sequence graphs.
• Motif and Repeat Search: Performs motif and repeat searches on the encoded dinucleotide-property data.
• Statistical Analysis: Supports statistical analyses on encoded physico-chemical profiles to detect genome-wide trends.

Scientific Applications:

• Genomic Research: Facilitates identification of conserved structural regions within genomes via physico-chemical profiling.
• Motif and Repeat Analysis: Enables detection of motifs and repetitive elements based on dinucleotide physico-chemical signatures.
• Statistical Genomics: Supports genome-wide statistical analyses of thermodynamic and geometrical properties for trend discovery.

Methodology:

DiProGB maps experimentally or literature-derived dinucleotide physico-chemical properties onto nucleotide sequences to generate sequence graphs and performs motif/repeat searches and statistical analyses on these encoded data using thermodynamical and geometrical property representations.