RSVP

RSVP (RNA Splicing Variant Predictor) predicts alternative isoforms of protein-coding genes by integrating genomic DNA evidence with aligned RNA-seq reads using open reading frame (ORF) graph models.

Key Features:

• ORF Graph Construction: Builds open reading frame (ORF) graphs that extend conventional splice graphs by incorporating transcriptional, splicing, and translational signals.
• Graph-Theoretic Isoform Prediction: Applies augmented graph-theoretic methods to combine genomic DNA evidence with RNA-seq alignments for improved isoform reconstruction.

Scientific Applications:

• Alternative Splicing and Isoform Discovery: Identifies and catalogs variant splice isoforms of protein-coding messenger RNAs from high-throughput RNA sequencing data.

Methodology:

RSVP constructs ORF graphs from RNA-seq read alignments, integrates genomic DNA sequence information and coding constraints, and applies graph-based algorithms to infer biologically consistent protein-coding gene isoforms.