Automated Primer-Blast like funcionnality

Question

[Eric Normandeau]

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!

[lyamwilly]

There is a tool called primertarget that does exactly what you need. http://www.genewide.com/

[erjo3868]

Eric, did primersearch solve your problem? I have the same question as you and haven't been able to find a good solution.

Answer 1

[Cameron Turner]

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

Answer 2

[JasonGans]

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

Answer 3

[Pierre Lindenbaum]

The ucsc contains a tool to run some electronic PCR: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

gfServer pcrDirect fPrimer rPrimer file(s).nib

there is also a standalone version of ncbi epcr: http://www.ncbi.nlm.nih.gov/tools/epcr/

[Eric Normandeau]

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?

[Pierre Lindenbaum]

see http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER may be you'll have to compile it from the sources ?

[onter]

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

Answer 4

[Prohan]

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.

[Eric Normandeau]

Thank you, I'll give primersearch a try.

[Camp]

Hey! Would you by any chance know of a script to run it on biopython? I've seen people saying it should be very straightforward all over but im finding it quite complicated given that i started learning python recently

Answer 5

[trausch]

Silica searches (multiple) PCR primers across entire genomes using primer3's thermodynamic calculations. It's an installation-free, open-source in-silico PCR web application: https://www.gear-genomics.com/silica/