Peptimapper

Peptimapper refines eukaryotic genome structural annotations by integrating proteomics-derived peptide sequence tags (PSTs) with translated genomic sequences to detect coding regions, validate exons and gene start sites, and identify novel protein-coding genes and splice isoforms.

Key Features:

• Identification of Novel Genes and Isoforms: Integrates proteomics data with genomic sequences to identify novel protein-coding genes and splice isoforms.
• Accurate Gene Start Sites and Exon Validation: Assigns correct gene start sites and validates predicted exons to improve gene structure representation.
• Cluster-Based Coding Region Detection: Maps peptide sequence tags (PSTs) onto translated genomic sequences and clusters closely located hits to detect potential coding regions with organism-specific optimization.
• Integration with Existing Annotations: Evaluates identified clusters against existing gene predictions from conventional genome annotation methods to inform annotation updates.
• Visualization and Data Integration: Exports cluster locations into GFF files for visualization in genome viewers.

Scientific Applications:

• Ectocarpus sp. proteogenomic annotation: Applied to the brown alga Ectocarpus sp., Peptimapper identified two potential novel genes (a ribosomal protein L22 and an aryl sulfotransferase), corrected the gene structure of a dihydrolipoamide acetyltransferase, and supported these findings with RT-PCR and transcriptomics data (ProteomeXchange PXD010618).

Methodology:

Maps peptide sequence tags (PSTs) onto translated genomic sequences, clusters adjacent PST hits to detect coding regions, evaluates clusters against existing gene predictions, and exports cluster locations into GFF for integration.