dotmatcher (EBI)

dotmatcher (EBI) generates threshold dotplots to compare two biological sequences and visualize regions of similarity for comparative sequence analysis.

Key Features:

• Threshold dotplot visualization: Produces threshold dotplots that display pairwise sequence matches above a specified threshold.
• Matrix-based sequence comparison: Constructs a matrix of pairwise matches and mismatches between two sequences for downstream visualization.
• Integration with EMBL-EBI resources: Supports linkage with UniProt, InterPro, ENA, and Ensembl Genomes datasets.
• Programmatic access: Offers RESTful and SOAP-based API access for incorporation into automated workflows.
• Enhanced visualization and job management: Provides improved visualization options and job management within the EMBL-EBI Job Dispatcher framework.

Scientific Applications:

• Comparative genomics: Visualizes sequence alignments to identify conserved sequences across organisms.
• Evolutionary studies: Reveals patterns of sequence similarity that support evolutionary analyses.
• Functional annotation: Highlights conserved motifs and potential functional domains for annotation.
• Structural motif detection: Aids detection of structural motifs through visualization of conserved sequence patterns.

Methodology:

Generates a matrix where each cell indicates a match or mismatch between sequence elements, applies a threshold to retain significant matches, and renders the retained matches as a dotplot.