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OligoChecker keeps a record of the oligos in your lab (or you can use the provided Excel template). You then just drop your sequence onto the program and OligoChecker outputs which of the oligos are suitable for PCR. Select two oligos and you are shown the alignment of the oligos on the sequence and the PCR product. To run a different PCR just click on another suitable oligo.

Do you have a print-out of your sequence with the position of the primers penciled in?

Are you using Excel to maintain a list of your oligos?

Have you just moved from working on one gene to working on a similar one and wonder which primers you more...

What's New

Version 2.40:
  • Layout: increased description field so that more text can be displayed
  • Layout: moved oligo order info to the right, made it hideable


Mac OS X 10.3 or later, Minimum display size 800x600.

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OligoChecker User Discussion

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Anotherhuman Member IconComment+0

Oligochecker fails to find many of the matching primer pairs. Especially when there are gaps during annealing. Is there any gap penalty option I missed somehow. A simple multiple sequence alignment script may have done that or not?

Reply1 reply
Version 2.40
Private (Developer)

If there are gaps then it is not a suitable primer. Unless I misunderstand what you are referring to.

HotScientist Member IconReview+11

I originally passed over OligoChecker due to a negative comment posted here by Taro Yamamoto, but some time later I saw it mentioned on a private site as only one of two programs with a "can't live without it" rating. So about 3 months ago I decided to give it a try after all. We have a filemaker database in our lab with over 2000 oligos which I exported as a tab delimited text file and import into OligoChecker. After 5 months of use I have to say:

1) I can't see any false results as Taro claims - as the description says OligoChecker won't deal with duplications in the gene (where the oligo can bind to several identical sites) but otherwise it works fine. And in hindsight his claim that the author doesn't know what the program is doing seems strange - after all he wrote it, didn't he?

2) OligoChecker certainly saves a LOT of time. It has now become a standard procedure for us to check a template against the oligo database before ordering oligos or performing any new PCR. You might not need it if you only have 10 oligos, but what if you have more than 100? Will you still remember where each binds? What about the oligos your colleagues ordered? We often find that we already have oligos we can use, thereby saving time and money.

3) We recently extended our work from mouse to other organisms. Without OligoChecker we might just have ordered new oligos for each gene, but with OligoChecker it is just a matter of seconds to find that many (but by no means all) oligos will work as PCR primers. I shudder to think of doing this by hand, and decided to register a lab license for OligoChecker afterwards (and found Dr. Winter to be a very pleasant person to deal with).

I would say that OligoChecker has become indispensable to me. Is it perfect? By no means. It is clearly a work in progress, but it has also been written with what the lab needs in mind. And it fits perfectly between Primer3 (which we use to design primers) and AmplifyX (Bill Engels excellent PCR simulation, for which OligoChecker has included export options for both the complete database and oligos suitable for PCR).

So our setup is:

Oligo design: Primer3

Oligo database: OligoChecker

PCR simulation: AmplifyX

I highly recommend it and would suggest that people make up their own mind.

P.S. A very welcome addition in the last update is that often used sequences can now be added to the menu for quick access.

Reply2 replies
Version 2.39.1

It has been 5 months, not 3 (that was a typo)

Private (Developer)

Thanks for the review. The website mentioned is probably Kristian's collection of biosoftware at


Anonymous Member IconReview

Thanks for the wondrously good program! This takes care of my oligos like no other program can.

Reply2 replies
Version 2.19.8
Anonymous Member Icon

Just wait till version 3 (out towards Christmas) :-)

Anonymous Member Icon

Btw there are PCR programs available which are far superior to OligoChecker when it comes to actually running a PCR simulation - Amplify (not AmplifiX) being the undisputed king - and I have a link to the Amplify website in my program. However all other programs have one big shortcoming - they are actually not that useful in the lab. Running a PCR simulation is a nice thing to have - but in the lab most of the time the question is not "how will my PCR look at the end" but "which oligos can I use for this template to begin with". That's why I wrote OligoChecker in the first place (and in time I hope to have all the functionality of Amplify too - and then some ;-)

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> 5 1


Current Version (2.x)


Downloads 3,401
Version Downloads 811
License Shareware
Date 19 Aug 2009
Platform OS X / PPC 32 / Intel 32
Price $19.95
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