Gexplora

Gexplora visualizes genomic element density along chromosomes to analyze distribution patterns of genes and transposable elements.

Key Features:

• Density Visualization: Plots the density of genomic elements using Gene Transfer Format (GTF) files, ideally sourced from Ensembl, to reveal regions with high concentrations of genes and transposable elements.
• Input Handling: Accepts annotated genomic data in GTF format for downstream density analysis.
• External Database Integration: Performs REST API calls to Ensembl, OMA, and STRING to retrieve sequence-intrinsic information, protein–protein interaction datasets, and orthologous group data.
• Chromosomal Hotspot Identification: Analyzes density profiles to pinpoint enriched chromosomal hotspots that may harbor genes associated with specific traits.

Scientific Applications:

• Candidate Gene Identification: Highlighting chromosomal regions of elevated element density to support selection of candidate genes linked to phenotypes.
• Trait Mapping: Pinpointing enriched regions that can be used in mapping loci associated with specific traits.
• Gene Distribution and Evolutionary Studies: Providing genome-wide views of gene and transposable element distributions for studies in evolutionary biology.
• Functional Genomics Integration: Combining density data with protein–protein interaction and orthology information to inform functional genomics analyses.

Methodology:

Accepting GTF files as input to compute and plot genomic element density along chromosomes; utilizing REST API calls to Ensembl, OMA, and STRING to fetch sequence-intrinsic information, protein–protein interaction datasets, and orthologous group data; analyzing density profiles to identify enriched chromosomal hotspots.