Question: Primer Specificity
1
gravatar for Surendra
7.8 years ago by
Surendra10
Surendra10 wrote:

how can i determine primer (upto 10bp) specificity in genome(prokaryotic and eukaryotic)?

primer • 7.3k views
ADD COMMENTlink modified 21 months ago by Felix Francis470 • written 7.8 years ago by Surendra10

Did you alread take a look at http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi ?

ADD REPLYlink written 7.8 years ago by Michael Schubert6.8k
3
gravatar for Sean Davis
7.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

For genomes available via the UCSC genome browser, you can use the In Silico PCR tool:

http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

ADD COMMENTlink written 7.8 years ago by Sean Davis25k
2
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

Did you try Primer-Blast ? http://www.ncbi.nlm.nih.gov/tools/primer-blast

Primer-BLAST was developed at NCBI to help users make primers that are specific to the input PCR template. It uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The blast results are then automatically analyzed to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause amplification of targets other than the input template.

ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum115k
0
gravatar for Wubin Qu
7.4 years ago by
Wubin Qu150
China
Wubin Qu150 wrote:

Try:

http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0/

or,

http://biocompute.bmi.ac.cn/MFEprimer/

ADD COMMENTlink written 7.4 years ago by Wubin Qu150

Please use the new server: http://www.mfeprimer.com/

ADD REPLYlink written 17 months ago by Wubin Qu150
0
gravatar for Felix Francis
21 months ago by
Felix Francis470
United States/University of Delaware
Felix Francis470 wrote:

Try ThermoAlign: A primer design tool for tiled amplicon sequencing (includes multiplexing) using highly specific primers.

Manuscript: http://www.nature.com/articles/srep44437

https://github.com/drmaize/ThermoAlign

ADD COMMENTlink written 21 months ago by Felix Francis470
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