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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. It can:
- Design primers to specifically amplify a template sequence or a set of related templates from a background nucleic acid population (BLAST database).
- Identify potential targets in a background nucleic acid population (BLAST Database).
| Primer 3 | BLAST |
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• 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: October 14, 2022