GAPP

GAPP profiles prokaryotic genomes using proteomic data to validate and refine gene models and to globally identify post-translational modifications.

Key Features:

• Comprehensive Genome Annotation: Validates existing protein predictions and refines gene models, including correction of translation initiation sites.
• Discovery of Novel Genes: Identifies novel protein-coding genes from proteomic evidence within prokaryotic genomes.
• Profiling of Post-translational Modifications (PTMs): Detects and catalogs a broad spectrum of PTMs, including reversible modifications, from proteomic datasets.
• Integration of Proteomic and Sequence Analysis: Integrates sequence analysis with experimental proteomic data through an algorithmic framework for cross-validation and discovery.

Scientific Applications:

• Helicobacter pylori proteogenomics: Applied to H. pylori proteomic data to confirm 84.9% of predicted proteins, identify 20 novel protein-coding genes, correct four translation initiation sites, and reveal extensive PTM events.
• Prokaryotic genome annotation and PTM discovery: Applicable to any sequenced prokaryotic organism for cross-validating predicted genetic models and globally profiling PTMs from proteomic data.

Methodology:

Leverages proteomic data to cross-validate predicted genetic models and discover PTMs, employing an algorithmic framework that integrates sequence analysis with experimental data.