Jul 21, 2025 · The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence …

Optimization of primer sequences for polymerase chain reaction (PCR) and quantitative PCR (qPCR) and reaction conditions remains an experimental challenge. We have developed a …

Primer-BLAST was developed at NCBI to help users make primers that are specific to intended PCR target.

We provide a concise overview of the main primer-related issues that confront anyone wanting to design a qPCR assay, consider the main criteria that have an impact on assay performance, …

Primer choice influences the estimated microbial composition. A set of different 16S rRNA gene sequencing primer pairs covering one, two, or three of the variable regions V1 to V9 is …

The option "Primer must span an exon-exon junction" will direct the program to return at least one primer (within a given primer pair) that spans an exon-exon junction.

For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus …

Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers. Primer-BLAST also supports placing primers based on …

Here, we describe a novel empirical-based method, miPrimer, which greatly reduces primer dimerization and increases primer specificity by factoring various intrinsic primer properties …

Jun 18, 2012 · We describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers. Primer-BLAST offers flexible options to adjust the …