Features

Advanced features in PrimerLab Genomic.

Feature Overview

These features are the foundation of PrimerLab’s design engine:

Batch Processing
Design primers for multiple target sequences in a single run. Supports FASTA input and parallel processing.
Tm Gradient Simulation
Simulate PCR performance across a range of annealing temperatures to find the optimal thermal cycling conditions.
Species Specificity
Ensure your primers bind only to the target species by cross-referencing against background genomes (e.g., Human vs. Pathogen).
Region Masking
Exclude specific regions (e.g., repeating elements, conserved domains) from design consideration.
Sequence Handling
Robust support for IUPAC ambiguity codes and automatic handling of RNA input sequences.

Validate your designs before ordering synthesis:

Off-target Detection
BLAST-based analysis to identify potential non-specific amplifications in the background genome.
In-silico PCR
Virtual amplification simulation to predict amplicon size and specificity.
Primer Compatibility Check
Analyze primer pairs for cross-dimers and self-dimers to prevent experimental failure.
Amplicon Analysis
Verify amplicon characteristics including GC content, secondary structures, and length constraints.

Specialized tools for quantitative PCR:

Probe Binding Simulation
Calculate thermodynamic properties for TaqMan probes to ensure efficient binding.
Melt Curve Prediction
Simulate SYBR Green melt curves to distinguish specific products from artifacts.
RT-qPCR Validation
Design primers spanning exon-exon junctions to avoid amplification of genomic DNA.

Report Generation
Export results in comprehensive Markdown, HTML, or machine-readable JSON formats.
Allele Discrimination
Scoring system for SNP genotyping primers to maximize discrimination capability.
Design History
Local SQLite database tracks every design run for complete reproducibility.