> ## Documentation Index
> Fetch the complete documentation index at: https://primerlab-genomic.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# Features

> Feature documentation: Features

Advanced features in PrimerLab Genomic.

## Feature Overview

### 🧬 Core Design Capabilities

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

* **[Batch Processing](batch-processing)**\
  Design primers for multiple target sequences in a single run. Supports FASTA input and parallel processing.

* **[Tm Gradient Simulation](tm-gradient)**\
  Simulate PCR performance across a range of annealing temperatures to find the optimal thermal cycling conditions.

* **[Species Specificity](species-specificity)**\
  Ensure your primers bind only to the target species by cross-referencing against background genomes (e.g., Human vs. Pathogen).

* **[Region Masking](masking)**\
  Exclude specific regions (e.g., repeating elements, conserved domains) from design consideration.

* **[Sequence Handling](sequence-handling)**\
  Robust support for IUPAC ambiguity codes and automatic handling of RNA input sequences.

### 🔍 Analysis & QC

Validate your designs before ordering synthesis:

* **[Off-target Detection](offtarget-detection)**\
  BLAST-based analysis to identify potential non-specific amplifications in the background genome.

* **[In-silico PCR](/docs/reference/cli/insilico)**\
  Virtual amplification simulation to predict amplicon size and specificity.

* **[Primer Compatibility Check](compat_check)**\
  Analyze primer pairs for cross-dimers and self-dimers to prevent experimental failure.

* **[Amplicon Analysis](amplicon)**\
  Verify amplicon characteristics including GC content, secondary structures, and length constraints.

### 🧪 Advanced qPCR & Probes

Specialized tools for quantitative PCR:

* **[Probe Binding Simulation](probe-binding)**\
  Calculate thermodynamic properties for TaqMan probes to ensure efficient binding.

* **[Melt Curve Prediction](melt-curve)**\
  Simulate SYBR Green melt curves to distinguish specific products from artifacts.

* **[RT-qPCR Validation](rtpcr)**\
  Design primers spanning exon-exon junctions to avoid amplification of genomic DNA.

### 🛠️ System & Utilities

* **[Report Generation](report-generation)**\
  Export results in comprehensive Markdown, HTML, or machine-readable JSON formats.

* **[Allele Discrimination](genotyping)**\
  Scoring system for SNP genotyping primers to maximize discrimination capability.

* **[Design History](/docs/reference/cli/history)**\
  Local SQLite database tracks every design run for complete reproducibility.