design primers across the target sequence · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

design primers across the target sequence

Hello,

I have a short target DNA sequence (40 nucleotides in length) in the given transcript DNA sequence. I wanted to design the PCR primers(reverse/forward) across this region. Is there any solution to do in biopython. If not, how can one do such analysis on NCBI-primer blast tool? Any suggestions or comments please? Thank you!

ncbi primer design primer3 biopython seqio

• 1,277 views • link

written 6.4 years ago by APJ •

https://www.ncbi.nlm.nih.gov/guide/howto/design-pcr-primers/

Check YouTube for additional tutorials if you learn visually.

• 0 views • link

written 6.4 years ago by GenoMax

I suggest you start by reading the documentation of PrimerBLAST.

• 0 views • link

written 6.4 years ago by ATpoint

If it helps? - A: primer design to discriminate sequences in intron-exon MSA

• 0 views • link

written 6.4 years ago by Kevin Blighe

0 answers

No answers yet.

Log in to answer this question.

More posts like this

PCR Primer Design Related
written 2.1 years ago by Bhavya •

Hello I was in the process of designing PCR primers. On the Exon 3----(2326..2824)= 499 bp .........of Human SERPING1 gene I used this sequence (downloaded …
Could you tell me why there are multiple peaks in the 16S V3-V4 tapestation data?
written 3.1 years ago by remi •

Hi researchers. I would like to know why my results of 1st PCR and 2nd PCR differ from illumina manual. https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf I ordered the forward …
18S gene not present in genome assembly?
written 4.7 years ago by milesdavis •

I am designing PCR primers to amplify a region of the 18S rRNA gene of Penicillium expansum. As the template for primer design, I use …
16S rRNA merge forward and reverse primers
written 5.1 years ago by ddowlin

Hi all, I have received 16S rRNA sequencing data for ~ 100 samples. I want to use these sequences to identify the samples to genus …
Tutorial: PCR Primer or Primer+Probe design
written 5.2 years ago by Kevin Blighe

Hi, I am pasting here the methods from a Standard Operating Procedure (SOP) that I wrote many years ago with a colleague for designing primers …
HOW to design a single strand primer
written 5.5 years ago by kumajis •

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 …
Tool to design Q-PCR primers with exon skipping?
written 6.5 years ago by gabriel.monteiro233 •

Hi, Say I want to design primers for Q-PCR for a gene with exons A, B, and C. My cells are grown in conditions in …
How to deal with inosines in primer sequences?
written 7.9 years ago by dom.byrne13 •

So I'm working on a problem which involves aligning PCR primers to a reference and then assessing the likelihood of those primers generating a successful …
Primer sequences after PCR, Assembly and PCR
written 9.5 years ago by s.kyungyong64 •

Hi, I think I am having trouble understanding PCR and trimming tools. After amplification using forward and reverse primers in PCR, wouldn't the resulting strands …
fastest method to get potential amplicons based on paired-primers
written 11.5 years ago by J.F.Jiang

Hi all, Generally, we can use tools such as primer3 to design the available primers for PCR. However, sometimes the primer will be located in …