VisProDom

VisProDom visualizes protein domains alongside transcriptional features across genomes to integrate genomic coordinates of protein domains and transcript structures for genome-wide analysis.

Key Features:

• R package implementation: Implemented as an R package that integrates annotated transcripts with protein domain annotations.
• Comprehensive database integration: Merges annotated transcripts with Pfam-derived protein domain annotations using a genome-wide database composed of 82 files combining GFF annotations with rpsblast tabular outputs.
• Genome-wide visualization: Produces visual representations of protein domains in the context of transcript structures across entire genomes.
• Simultaneous multi-genome screening: Enables screening across multiple genomes for specific protein domains or transcript names to support comparative analyses.
• Custom data input: Accepts user-supplied genome datasets for integration with built-in annotations.

Scientific Applications:

• Molecular evolution: Visualizes domain and transcript architecture to investigate functional variation and evolutionary changes at the protein and transcript levels.
• Comparative genomics: Supports cross-genome comparison of protein domains and transcript structures to explore evolutionary patterns and functional variation among species.

Methodology:

Implemented as an R package that integrates annotated transcripts with Pfam-derived protein domain data by processing 82 files combining GFF annotations and rpsblast tabular outputs to generate genome-wide visual representations.