VESPA

VESPA integrates peptide-centric proteomics and transcriptomics with genomic coordinates to improve structural annotation and detect mis-annotations in prokaryotic genomes.

Key Features:

• Integration of multi-omics data: Integrates peptide-centric proteomics with transcriptomic data from global microarrays or RNA-Seq and maps both data types to genomic coordinates.
• Multi-resolution visualization: Provides visualization at three levels of genomic resolution to correlate proteomics and transcriptomics with gene structure and genomic context.
• Linked search and data interrogation: Enables linked searches against mapped data to identify genomic regions with a high likelihood of structural mis-annotation.
• Data export for external analysis: Search results and mapped evidence can be exported for downstream analysis and external validation.
• Concurrent BLAST examination: Potential coding regions identified by integrated evidence can be examined concurrently using BLAST for functional and homology assessment.

Scientific Applications:

• Genome curation: Supports identification and correction of structural mis-annotations in prokaryotic genome annotations using integrated proteomics and transcriptomics evidence.
• Demonstrated use cases: Applied to studies of Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002 to rapidly pinpoint and investigate annotation errors.

Methodology:

Implemented as a desktop Java™ application that handles large heterogeneous datasets on the client side and integrates proteomics and transcriptomics into a cohesive genomic visualization framework.