TipMT

TipMT designs taxon-specific PCR primers from genomic data for genotyping by identifying single sequence repeats (SSRs) and orthologous/taxa-specific genes suitable for Multiplex PCR.

Key Features:

• Genomic-data-based primer search and design: Uses user-provided genomic data to search and design primers for genotyping.
• Targeted primer design: Identifies single sequence repeats (SSRs) and orthologous/taxa-specific genes to produce taxon-specific primers suitable for Multiplex PCR.
• High-throughput automation: Supports high-throughput primer design and processing for large-scale genotyping studies.
• Experimental validation: Validated with genomic data from Leishmania species (L. amazonensis, L. braziliensis, L. infantum, L. major) and experimentally tested by PCR using artificial genomic DNA mixtures to demonstrate species discrimination.

Scientific Applications:

• Clinical and environmental diagnostics: Enables the design of specific primers for molecular diagnostic assays in clinical and environmental samples.
• Pathogen identification: Supports development of primers to discriminate between pathogen species.
• Biodiversity and evolutionary studies: Facilitates marker selection for biodiversity assessments and evolutionary analyses.

Methodology:

Users input genomic data; the tool identifies SSRs or orthologous/taxa-specific genes suitable for primer design; primers are designed to ensure specificity and suitability for Multiplex PCR.