in silico PCR of designed primers against an assembled transcriptome
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5.1 years ago

Dear all, I have designed some Primers from several genes of an assemled transcriptome. I need to check that these primers are specific, so I want to do In silico PCR these primers against the transcriptome. Do you know any tools that do this job? I tried some tools like : NCBI-ePCR, EmBoss, genome tester, ... but they did not work for me.

RNA-Seq E-PCR • 1.9k views
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5.1 years ago
Erik Wright ▴ 380

The R package DECIPHER can be used to perform in silico PCR. The function AmplifyDNA takes in a set of (typically 2) primers and a DNAStringSet of templates, and returns all possible amplicons ranked by their predicted amplification efficiency. Enter ?AmplifyDNA in R for more information. Hope that helps!

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Dear Wright, Thank you for the answer. How can I make a DNAStringSet of the templates. I want all the transcripts as the template.

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You can use readDNAStringSet to create a DNAStringSet from a FASTA or FASTQ sequence file.