SplicingGraphs

SplicingGraphs constructs and analyzes graph-based representations of all splicing variants based on gene models to represent alternative splicing and enable RNA-seq and EST read assignment and summarization.

Key Features:

• Graph-Based Representation: Represents all splicing variants of a gene as paths within a graph, capturing relationships and structural patterns among transcripts.
• Splicing Graph Construction: Builds splicing graphs that encapsulate the full spectrum of alternative splicing events and transcript diversity for each gene.
• Visualization and Manipulation: Visualizes splicing graphs and associated "bubbles" that correspond to alternative splicing events and supports manipulation of graph elements.
• RNA-seq Read Assignment: Assigns RNA-seq reads to specific edges within splicing graphs to support analysis of transcript expression levels and variant prevalence.
• Summarization Capabilities: Provides methods to summarize assigned RNA-seq data across graph elements to derive expression-level insights.

Scientific Applications:

• Alternative splicing analysis: Facilitates study of alternative splicing mechanisms by representing and comparing all splice variants within a unified graph.
• Gene regulation and disease studies: Enables investigation of splicing alterations underlying gene regulation and disease by mapping RNA-seq and EST evidence to graph structures.
• Analysis of genes with extensive transcript diversity: Simplifies analysis of genes with large numbers of transcripts by providing a holistic graph view rather than separate linear assemblies.

Methodology:

Assembles expressed sequence tag (EST) reads directly into the splicing graph rather than assembling EST reads for each splicing variant individually.