I am trying to design a set of primers to cover the coding region of a gene. I have looked at Exon Primer, but it doesn't really do what I want:
1) To design to strict size limits, i.e. the amplicon should be < 200bp
2) To stick to a very rigid Tm, i.e. 60 C
3) To split the exon designs into multiple parts if the design template is too long
Exon Primer doesn't seem flexible enough to do this - any other suggestions (other than doing it manually).
At Ghent University, we have specifically developed a tool for that, called primerXL (http://www.primerxl.org). We have used it to make assays for the entire human exome (http://www.pxlence.com).
http://www.primerxl.org
I use Primer 3 for my primer design which can restrict oligos to the parameters that you're describing, however you have to make the primers one at a time. http://bioinfo.ut.ee/primer3-0.4.0/
In addition to my answer, I'm assuming you're looking for something to make a design quickly with little manual input. While I can appreciate that, in my opinion there is no replacement for custom primer design with some manual input. I use primer 3 for all my design and my primers work pretty much 8 times out of 10. It takes a little more time for sure, but in my experience, it gets me better results.
Thanks. ExonPrimer uses Primer3, so it's not quite what I'm looking for
For genomic / gene expression I use NCBI. The main point of it is that it's coupled directly into Blast to test for specificity against your genome... But it lets you set all those params too yes.
http://biotools.umassmed.edu/bioapps/primer3_www.cgi
Primer3 has been working fine for me so far
You can download "Geneious R7" by clicking on the link below:
http://www.geneious.com/download
Register with your email account. You don't need any license/serial key for first 15 days as it is free.
I use Geneious R7 for designing primers and its a very nice tool. With the help of this tool I designed 6 sets of primers and all worked very fine.
You can download "Geneious R7" by clicking on the link below:
http://www.geneious.com/download
Register with your email account. Its free for first 15 days.
At Ghent University, we have specifically developed a tool for that, called primerXL (http://www.primerxl.org). We have used it to make assays for the entire human exome (http://www.pxlence.com).
http://www.primerxl.org
Thank you so much! If I could rate up your post more I would - a very useful tool. I am, as you have guessed, designing a panel of amplicons for targeted resquencing using a Fluidigm Access Array. I therefore need quite rigid conditions for it to work.
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