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What is Primer-BLAST?

Primer-BLAST is a combination of Primer3, a popular primer designing tool, and NCBI BLAST. 
  • Primer-BLAST has two basic modes.
    1. Design primers to specifically amplify a template sequence or a set of related templates from a background nucleic acid population (BLAST database).
    2. Identify potential targets in a background nucleic acid population (BLAST Database).

Image of Primer3 and BLAST webpages

Primer 3 BLAST

•  Designs primers and internal oligos

• Matches primer and template Tm

•  Allows template target region selection

• Checks primers for secondary structure, self-complementarity, clamp sequence etc.

• Can screen for interspersed repeats

•  Non-stringent BLAST search of target database (background)

• Filtering and reporting potential off-target matches

• Provides alignments and links to potential products

•  Includes annotation information for NCBI RefSeqs

• Exon / Intron structure

• SNP avoidance

•  Aligns multiple targets for common primer selection

Last Reviewed: September 22, 2023