Question: Template-specific primers design
1
gravatar for Artem Kiselev
4.1 years ago by
Russian Federation
Artem Kiselev20 wrote:

I'm looking for some PCR primers design tool (or pipeline) that can do reference-dependent, template-specific primers design, a good example of this approach is NCBI-Primer-Blast, but it's not possible to run batch-job on NCBI servers, and I can't run this tool local.

I found the JCVI Primer Designer project but it's from one hand is dead, and the other hand is not completed yet.

ADD COMMENTlink modified 11 days ago • written 4.1 years ago by Artem Kiselev20
1

You can design primers with you favorite software and then check for specificity with primersearch from Emboss http://emboss.bioinformatics.nl/cgi-bin/emboss/help/primersearch

ADD REPLYlink written 4.1 years ago by Biomonika (Noolean)3.0k

would primer3 suit your needs? source code is available for you to run locally, although you may need to build a pipeline around it to feed it reference sequence.

ADD REPLYlink written 4.1 years ago by Katie D'Aco970

Of course I know Primer3, but it can't perform primers alignment on chosen genome or mRNA for specificity check.

ADD REPLYlink written 4.1 years ago by Artem Kiselev20
1

I think primer3 uses a heuristic to estimate genome wide specificity (could be wrong about that). Have you seen PRIMEGENS? Not sure how it works, but it looks like it takes a reference sequence as a parameter.

ADD REPLYlink written 4.1 years ago by Katie D'Aco970

I have completed testing of PRIMEGENS tool (it looked very promising), but unfortinatly web version of this tool work only on test data provided by developer and standalone tool not comleted yet (has limited functionality)...

ADD REPLYlink written 4.1 years ago by Artem Kiselev20
1
gravatar for Felix Francis
18 months ago by
Felix Francis450
United States/University of Delaware
Felix Francis450 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 18 months ago by Felix Francis450
0
gravatar for Artem Kiselev
11 days ago by
Russian Federation
Artem Kiselev20 wrote:

I founded the tool for this task, PrimerWay, please use:

https://github.com/zoldrax/primer-way

ADD COMMENTlink written 11 days ago by Artem Kiselev20
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