RJPrimers

RJPrimers identifies unique repeat junctions in eukaryotic genomes and designs primers for repeat junction markers (RJMs) using BLASTN searches against annotated repeat databases and a dedicated junction-finding algorithm. It enables genome-wide marker development for large and complex genomes.

Key Features:

• Repeat Junction Identification: Detects junctions formed by transposable element insertions, including cut-and-paste and copy-and-paste mechanisms, through BLASTN-based screening of annotated repeat databases.
• Automated Primer Design: Generates primers for unique repeat junctions using Primer3 and BatchPrimer3 for high-throughput marker development.

Scientific Applications:

• Genetic Mapping and Diversity Analysis: Produces genome-wide repeat junction markers for genetic diversity assays and genetic and physical mapping in species such as rice and Aegilops tauschii.

Methodology:

RJPrimers performs BLASTN searches to identify repeat-associated sequences, applies a repeat junction detection algorithm to define unique junction sites, and uses Primer3 and BatchPrimer3 to design specific primers for validated repeat junction markers.