Deform-nu

Deform-nu predicts nucleosome positioning from DNA sequences using a DNA deformation energy model to estimate nucleosome occupancy and rotational positioning for studies of chromatin structure and gene regulation.

Key Features:

• DNA deformation energy model: Implements a deformation energy model to relate DNA physical properties to nucleosome placement.
• Nucleosome occupancy estimation: Estimates nucleosome occupancy along DNA sequences based on calculated deformation energies.
• Rotational positioning estimation: Predicts nucleosome rotational positioning as inferred from the deformation energy model.
• Sequence-based analysis: Operates on input DNA sequences to derive deformation energy profiles and positioning predictions.
• Validation: Includes validation examples demonstrating accuracy of predicted nucleosome positions.

Scientific Applications:

• Chromatin structure and function: Inform analyses of nucleosome organization and chromatin architecture.
• Gene expression regulation: Support studies linking nucleosome positioning to transcriptional regulation.
• DNA replication and repair: Aid investigations of how nucleosome placement influences replication and repair processes.
• Epigenetics: Contribute to research on epigenetic regulation mediated by nucleosome positioning.
• Chromatin biology: Serve studies focused on nucleosome dynamics and chromatin-related mechanisms.
• DNA–protein interaction studies: Provide positional context for analyses of DNA-binding proteins and nucleosome-associated factors.

Methodology:

Computes DNA deformation energy from input DNA sequences using a deformation energy model to estimate nucleosome occupancy and rotational positioning.