MorphoCatcher

MorphoCatcher identifies taxon-specific polymorphic regions in orthologous genes and viral genomes to guide design of loop-mediated isothermal amplification (LAMP) primers for nucleic acid detection in agricultural and medical diagnostics and integrates with PrimerExplorer (Eiken Chemical Co., Ltd., Tokyo, Japan).

Key Features:

• Multiple-Alignment Based Search: Performs multiple-sequence alignments of orthologous genes or viral genomes to detect taxon-specific mutations and polymorphic regions.
• Visual Screening and Selection: Provides visual screening of alignments to support selection of target sequences with high densities of taxon-specific mutations.
• Informative Sliding-Window Plot Analysis: Computes sliding-window plots across multiple alignments to identify informative regions and ensure primer ends cover mutation-rich segments.
• Integration with PrimerExplorer (Eiken Chemical Co., Ltd., Tokyo, Japan): Exports selected target sequences to PrimerExplorer for LAMP primer design.

Scientific Applications:

• Molecular diagnostics: Enables development of LAMP assays with high specificity and sensitivity for pathogen and taxon detection in clinical settings.
• Agricultural pathogen detection: Supports identification and differentiation of crop pathogens to inform disease management and control.
• Viral surveillance: Facilitates design of taxon-specific assays for viral genome identification and monitoring.

Methodology:

Performs multiple-alignment based searches of orthologous genes or viral genomes to identify taxon-specific mutations, enables visual screening of alignments, generates sliding-window plot analyses to locate informative regions, selects target sequences for primer design, and exports targets to PrimerExplorer.