DNAshape

DNAshape predicts DNA structural features from nucleotide sequences and genomic coordinates to enable analysis of DNA shape influences on genomic function and to produce feature matrices for computational modeling.

Key Features:

• High-Throughput Capability: Performs high-throughput prediction of DNA structural features for large-scale genomic datasets.
• Input Flexibility: Accepts nucleotide sequences and genomic coordinates as input.
• Graphical Representations: Generates graphical outputs that visualize predicted DNA shape features.
• Feature Encoding: Encodes DNA sequence and shape features into user-defined combinations of k-mer sequences and DNA shape attributes to create feature matrices.
• Integration with Machine Learning: Produces feature matrices compatible with machine learning software packages for predictive modeling.

Scientific Applications:

• Epigenetic Studies: Facilitates exploration of relationships between DNA shape and epigenetic modifications.
• Gene Regulation Analysis: Supports identification of structural motifs that influence gene expression and regulatory interactions.
• Genomic Annotation: Enables annotation of genomic regions based on predicted DNA structural characteristics.

Methodology:

Uses the DNAshapeR package implemented in the R programming language to predict DNA shape features, generate graphical outputs, and encode sequence and shape information into k-mer–based feature matrices.