Question: Automated Primer-Blast like funcionnality
gravatar for Eric Normandeau
4.7 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

A member of our lab is using Primer-Blast ( to find what DNA her pairs of primers amplify in the NT nucleotide database. She designed degenerated primers and the number of possible pairs goes up to 256. She does not want to do that many primer-blasts by hand, obviously, and Primer-Blast apparently cannot use degenerate primers. I am therefore looking for a tool to automate these primer blasts.

Is there a command-line interface tool that would, given a local database of nucleotide sequences, return which sequences would amplify with a given pair of primers? It does not look like Primer-Blast can be downloaded for local and I don't think Primer3 can be used for that purpose.

My idea is to automatically generate all possible degenerate primer pairs and then run the CLI tool on them. If a program was able to directly use degenerate primers, that would be even awesomer :)

Thanks for your suggestions!

ADD COMMENTlink modified 4.5 years ago by Cameron Turner30 • written 4.7 years ago by Eric Normandeau10k

There is a tool called  primertarget that does exactly what you need.


ADD REPLYlink written 4.6 years ago by lyamwilly0
gravatar for Cameron Turner
4.5 years ago by
United States
Cameron Turner30 wrote:

primerTree ( is the closest thing I've found to a command-line interface for Primer-BLAST. Here's the R package on CRAN:  The primer_search command can use primers with IUPAC codes.

ADD COMMENTlink written 4.5 years ago by Cameron Turner30
gravatar for Pierre Lindenbaum
4.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:
The ucsc contains a tool to run some electronic PCR:
gfServer pcrDirect fPrimer rPrimer file(s).nib
there is also a standalone version of ncbi epcr:
ADD COMMENTlink written 4.7 years ago by Pierre Lindenbaum118k

Pierre, there are quite a bunch of tools listed at your first URL. None contain 'pcr' or 'primer' and the two that contain 'blast' are not what I am looking for. Would you have specific names for the tools you are thinking about?

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Eric Normandeau10k

see may be you'll have to compile it from the sources ?

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum118k

The gfServer tool is under the blat/ folder at Pierre's link (I realize this is 5 months after the fact, but fwiw)

ADD REPLYlink written 4.2 years ago by gareth86290
gravatar for Prohan
4.7 years ago by
United States
Prohan350 wrote:

Hi I've found the EMBOSS tool "primersearch" to be the most straightforward - for whatever reason they don't call it an in-silico pcr tool but that's what it does.

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Prohan350

Thank you, I'll give primersearch a try.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Eric Normandeau10k
gravatar for JasonGans
4.6 years ago by
United States
JasonGans100 wrote:

ThermonucleotideBLAST ( will search degenerate PCR primers against a fasta file (or BLAST-formatted nucleotide sequence database).

ADD COMMENTlink written 4.6 years ago by JasonGans100
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