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 databases and …

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

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

Mar 28, 2025 · Its final output summarizes the lead forward and reverse primer pair for each target site, a measure of the likelihood of binding to off-targets, and additional information to aid decision-making.

If there is a high requirement for certainty, PCR products can also be sequenced to confirm primer specificity in further. Other important requirements for primers are the Tm (melting temperature) …

To find primers for a group of related sequences, Primer-BLAST aligns the longest sequence to the rest to find common regions. It uses these to limit the locations of primers. The longest sequence is also …

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 specificity …

Settings and designed primer sequences can be stored locally for later use. Primer3Plus supports a range of common sequence formats, such as FASTA. Finally, primers selected by Primer3Plus can …

Jun 28, 2017 · The good news is that an existing tool, Primer-BLAST, fills in nicely for the functions of both Forward and Reverse e-PCR, and has the additional benefit of de novo primer design.

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 commonly …