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 can still use for your PCR? Do you subclone and rearrange sequences and somewhere along the line lost track on which primer to use where? Have you started in a new lab, inherited a box of oligos and a folder full of printouts that came with them but no information on what they were ordered for? Have you ordered and waited for primers because you don't know which of the ones available you can use with your sequence? If any of these sound familiar then OligoChecker might be for you.
This review was originally posted on VersionTracker.com. I originally passed over OligoChecker due to a negative comment posted on MacUpdate 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.
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