I want to design a primer only for a single strand (forward or reverse but not both) because the target is a fusion gene and not sure what fusion sequence is.
For most primer design tools is set for two primer design (like primer blast or primer3 which conside compartblity for both primer), is there some method for just design one primer and consider specificity on the whole genome.
1 answer
Its possible to tell primer3 to design only one primer. Just below the sequence input box there are tick boxes for "Pick left primer", "Pick hybridization probe", "pick right primer". By default both "Pick left primer" and "Pick right primer" are selected, but you can unselect one if you only want to design one primer.
You will then need to manually check the primer for uniqueness by blasting it or blatting it yourself.
Log in to answer this question.
-
16S rRNA merge forward and reverse primers
written by ddowlin
-
design primers across the target sequence
written by APJ •
-
Tool to design Q-PCR primers with exon skipping?
written by gabriel.monteiro233 •
-
Validate PCR DNA primers against whole de novel genome
written by qwzhang0601
-
Tool: PrimerServer: a high-throughput primer design and specificity-checking platform
written by bill-zt •
-
Primer sequences after PCR, Assembly and PCR
written by s.kyungyong64 •
-
Checking primers against many target genes, with mismatch tolerance
written by rotem •
-
fastest method to get potential amplicons based on paired-primers
written by J.F.Jiang
-
Check For Primer Mixing
written by David A. •
-
Cross Reactor Script
written by User 7351 •
