jPCR

jPCR performs PCR primer design and virtual PCR simulation to support design, evaluation, and optimization of primers and probes for diverse PCR applications including standard, multiplex, long-distance, inverse, real-time, unique and group-specific assays, bisulfite modification assays, polymerase extension PCR (OE-PCR) for multi-fragment assembly cloning, and microarray design.

Key Features:

• Comprehensive Primer Design: Designs primers and probes for standard PCR, multiplex PCR, long-distance PCR, inverse PCR, real-time PCR, unique and group-specific assays, bisulfite modification assays, polymerase extension PCR (OE-PCR) for multi-fragment assembly cloning, and microarray probes.
• Virtual PCR Simulation: Simulates PCR on linear and circular DNA templates to predict amplicons and evaluate assay outcomes in silico.
• Primer and Probe Analysis: Predicts sensitivity and specificity by searching databases for optimal mismatches, sequence similarity, and stability, determines primer location and orientation, estimates binding efficiency, and calculates melting temperatures for standard and degenerate oligonucleotides.
• Batch File Processing: Supports batch processing of sequence files for high-throughput primer and probe design and analysis.
• Database Integration: Searches large and small sequence databases to identify candidate primer and probe sequences.

Scientific Applications:

• Molecular biology and genetics: Enables primer design and virtual PCR for experiments across standard, multiplex, long-distance, inverse, and real-time PCR workflows.
• Molecular diagnostics: Supports development and evaluation of diagnostic assays, including unique and group-specific and real-time PCR assays.
• Bisulfite modification assays: Facilitates primer design and evaluation for bisulfite-modified DNA assays.
• OE-PCR and multi-fragment assembly cloning: Assists design of primers for polymerase extension PCR (OE-PCR) used in multi-fragment assembly cloning.
• Microarray design and high-throughput studies: Supports probe and primer selection and batch processing for microarray design and large-scale genomic analyses.

Methodology:

Performs in silico analysis of nucleic acid sequences by assessing sequence mismatches, similarity, stability, binding efficiency, and melting temperatures, integrates database searches to identify candidate sequences, and simulates PCR on linear and circular DNA templates.