Recently I saw that the Sol Genomics webpage has taken down the option of doing In silico PCR for Arabidopsis. While I have found many programs that allow you to utilize an input sequence, these are typically designed for a specific locus. I need to use a program that will analyze the whole genome. I'll settle for CDS sequences alone, but I haven't had any luck finding anything recently. Thanks for any help you can provide!
Hi Tami,
Are you just interested in checking the binding sites of existing primers or in primer design as well? I wrote a Python script to calculate PCR product sizes for different accessions. This script searches for additional (unwanted) binding sites of the primers as well. You could have it if you do not need much more functions.
Best,
Boas
Hi Tami,
You can try fastpcr, the whole genome can be loaded on the software in order to test your primers or design new ones.
Best,
Yair
Hi Boas,
I'm basically trying to test whether primers I've designed are binding to a specific locus and generating only one amplicon of the size I expect. I'm trying to use Yair's suggestion of fastpcr first, but thanks for answering. I appreciate the help.
Best,
Tami
Recent update: For anyone following this Sol Genomics (solgenomics.net) recently put the Arabidopsis thaliana resources back online in their in silico PCR tool.
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