Hi, does anyone have a method for in silico PCR? In other words, I have two primers and a genomic sequence and would like to have a prediction of a PCR result. A BioPerl solution would be perfect, but I won't snub my nose at other solutions. Thank you.
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Try Jim Kent's isPCR (which is the executable for UCSC's PCR mentioned by Pierre):
Source is here (zip file). Executables for different platforms are here.
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Casey Bergman
Hi Lee. There is documentation in the README in this source directory, but as an alternative I've added a link to compiled executables. Inside the relevant directory you will find an isPcr.zip file which should run out of the box if you've chosen the right platform.
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Casey Bergman
Easy to install if you are using conda, ispcr was packaged for bioconda: https://anaconda.org/bioconda/ispcr
There's a perl wrapper for primer3: http://www.bioperl.org/wiki/Module:Bio::Tools::Run::Primer3
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Pierre Lindenbaum
... but I think the two first would be better for a whole genome.
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Pierre Lindenbaum
Thanks for posting this Wubin, it looks like a nice system that I wasn't aware of.
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Casey Bergman
Please use the new server: http://www.mfeprimer.com/
I was directed here from seqanswers. Actually the best strategy is to use short-read mappers. Checking primer uniqueness is exactly the same as mapping Illumina paired-end reads. The short-read mappers are very fast and accurate. They also check mismatches and indels.
Yes, but then you need to figure out the orientation of the primers and their relative distance which is additional work.
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Biomonika (Noolean)
I said "paired-end". Illumina paired-end reads have the same orientation as primers. The insert size of a read pair is exactly the same as the length of the PCR product. With a short-read mapper supporting paired-end mapping, you need to do little additional work while benefiting the speed, accuracy and sensitivity of mainstream short-read mappers which are usually more sophisticated.
I am using command line version of primersearch. It outputs all amplicons and size of the products.
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Biomonika (Noolean)
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Has anyone used this method? Does it work? http://biodoc.ist.unomaha.edu/wiki/In-silico_PCR#Methodology