Gepard

Gepard generates dotplots for comparing genomic sequences to visualize sequence similarity and structural variation.

Key Features:

• Efficient Calculation: Employs suffix arrays to compute dotplots with time complexity Theta(m*log n).
• Client-Server Mode: Implements a client-server architecture enabling remote dotplot calculation without requiring pre-download of full sequence or annotation datasets.
• Functional Annotation Coloring: Supports coloring of dotplots based on functional annotations to highlight annotated elements in sequence comparisons.

Scientific Applications:

• Comparative Genomics: Visualizing sequence similarities and differences between genomes.
• Genome Rearrangement Analysis: Detecting and visualizing genome rearrangements.
• Evolutionary Relationship Inference: Assessing evolutionary relationships via sequence similarity patterns.
• Genomic Duplication Detection: Identifying and visualizing genomic duplications.

Methodology:

Uses suffix arrays for efficient string matching, yielding Theta(m*log n) time complexity for dotplot generation.