BioCantor

BioCantor provides Python-based functionality for arithmetic and conversion of genomic features across genomic, transcript, and protein coordinate systems to enable precise feature manipulation and annotation.

Key Features:

• Coordinate system abstraction: Represents arbitrarily related coordinate systems enabling conversion and manipulation between genomic, transcript, and protein coordinates.
• Feature arithmetic and operations: Implements a wide range of operations on genomic features and supports feature arithmetic across coordinate frames.
• Input/output support: Supports reading and writing various file formats to integrate with different data sources.

Scientific Applications:

• Variant annotation: Enables precise mapping of variants between genomic, transcript, and protein coordinates for annotation tasks.
• Gene expression analysis: Supports analyses that require coordinate conversions and feature-level manipulations for gene expression studies.
• Protein structure prediction: Facilitates mapping between transcript and protein coordinates relevant to protein sequence and structure analyses.
• Genomic feature manipulation and annotation: Provides a unified framework for precise manipulation and analysis of genomic data across coordinate systems.

Methodology:

Implemented as a Python 3 library with minimal external dependencies and built on an abstraction of coordinate systems to perform feature arithmetic and coordinate conversion.