OligoChecker X - 2.40

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.

StuffIt 8 (even 8.0.2) has a problem with StuffIt 9 files. Please make sure you are using an up-to-date version.

... as my girlfriend started her new job as research associate she brought an Excel spreadsheet with the oligo data from her new lab with her. We transferred the 145 oligos into OligoChecker in just under 3 minutes using the Excel template. Her boss had designed some oligos to introduce mutations into a sequence so we ran the oligos against the sequence - they look fine EXCEPT THERE ARE NO MISMATCHES IN THE ALIGNMENT! The oligos her boss designed and bought are not mutagenic! Time saved before the mistake would have been discovered by sequencing the "mutated" plasmid: about a week. Money saved: about $1,000. :-)

then make sure you don't use StruffIt 8.0 - the version 8.0 of stuffit expander has a known problem of not setting the permissions correctly. The solution is to upgrade to stuffit expander version 8.0.2 which fixes the problem.

for reasons I don't understand yet it doesn't run properly on 10.1 systems - that is it works fine but it does not display the PCR products properly