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 OligoChecker X - 2.39.1organize & better utilize oligos in the lab, run PCR |
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Product Description:
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.
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.
What's new in this version:
- 2.39.1
- added more isotope data
- 2.39.0
- added calculation window for radioactive decay
- 2.38.4
- added calculation window for mixing solutions
- fixed bug in registration window
- updated website info for other scientific apps
- added link to AmplifX
- added "companies" and "software" menu
- renamed butons to more accurately reflect their function
- added menu "Please inform me about new releases"
- 2.38.3
- preferences no longer get lost
- Calculate effect of single-base changes
- Calculate % correct PCR product for template of lenght x after n rounds of amplification for different Polymerases
- keep often used sequences in a Sequences menu for easy access
- Clean up sequences (e.g. keep only GATC or IUPAC codes)
- more info windows
- check for updates menu
- known problems:
- German localization only partly done
Operating System Requirements:
This product is designed to run on the following operating systems:
- Mac OS X 10.5 Intel
- Mac OS X 10.5 PPC
- Mac OS X 10.4 Intel
- Mac OS X 10.4 PPC
- Mac OS X 10.3.9
- Mac OS X 10.3
- Mac OS X 10.2
Additional Requirements:
- Mac OS X 10.2 or higher
Screenshots:
Download Links:
Download OligoChecker X Now (File Size: 6.2M)
Your Installed Versions:
Feedback Summary:
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Featured Reviews
Recommended 
- Version: 2.39.1, 8/31/2008 02:42PM PST
HotScientist
Most Recent Replies: View All 1 Replies
- Recommended
Download link working again - Version: 2.20.5, 3/5/2006 05:19AM PST
MarkusWinter (Markus Winter)
For unknown reasons the download link reverted to the old link resulting in a 404 site not found error - it's fixed now (thanks to Meadow for the notice)
It seems ... - Version: 2.10.2, 2/3/2005 12:18PM PST
MarkusWinter (Markus Winter)
StuffIt 8 (even 8.0.2) has a problem with StuffIt 9 files. Please make sure you are using an up-to-date version.
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.