in silico PCR of designed primers against an assembled transcriptome

Question

[ahmad.iut]

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.

Thank you in advanced

Answer 1

[Erik Wright]

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!

[ahmad.iut]

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

[Erik Wright]

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