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 OligoChecker - 2.21.25organize & 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:
- added "make selected text uppercase"
- added "make selected text lowercase"
- changed all text fields to conform with standard behaviour (select all works)
- added speech feedback to input of oligo sequences
- added readback of oligo sequences (or just the selected part)
- fixed: if the sequence contained numbers then these were also shown in the PCR product
- added "Keep only GATC" to Edit menu (works on selected text in a sequence)
- added "Keep only IUPAC codes" to Edit menu (works on selected text in a sequence)
- added "Keep only extended IUPAC codes (includes 4,5,6)" to Edit menu (works on selected text in a sequence)
- cleaned up tab order in oligo window
- added "Reverse selected sequence" to Edit menu (works on selected text in a sequence)
- added "Invert selected sequence" to Edit menu (works on selected text in a sequence)
- added "Complement selected sequence" to Edit menu (works on selected text in a sequence)
- added option "Speak on entry" to Edit menu
- try to merge custom speech classes and custom DNA sequence field classes - not working well
- changes to ListBox background colouring in REALbasic require modification in my code - implemented
- separated custom "speech class" and "DNA sequence class" again
- start implementing a new recognition algorithm that deals with degenerate codes
- got new recognition algorithm that deals with degenerate codes working (albeit too slowly at the moment)
- added option to select allowed DNA codes (GATC only, IUPAC, or extended IUPAC)
- improved calculation of position of selected sequence text
- fixed a bug where non-DNA characters in the DNA sequence could prevent suitable oligos to be found
- fixed that dropping a new sequence would still leave "x suitable oligos found" on top of the result box
- added option to change text size of the controls and fields
- added HelpTags
- fixed some mistakes in the help texts
- made size of Listbox with selected oligos dependend on which platform it is run on (in order to accommodate larger font on Windows)
- added option to turn help tags / tips on and off
- changed default font for Windows from "System" to "Arial" as the system font does not scale properly on Windows, e.g. font sizes 1-12, 13-15, 16-17, 18-21, etc. are all displayed the same. So going from size 9 to 12 on Windows changes nothing. Arial was chosen as it is the only easily readable font that is available on all Windows platforms.
- fixed a bug where changes to the text size did not work correctly
- Fixed a bug where changing the font size would leave display artefacts on screen
- added more data to Nucleotide info window
- fixed a bug where a sequence dropped onto the sequence field was not shown until the window was active
- Streamlined code (removed duplicate code segments)
- modified highlight behaviour of listboxes to emphasize selection
- made sequence window in "Measure Oligo Concentration" Window multiline to accommodate long oligos
- Found bug in Windows version (Preference file not found)
- Cleaned up Nucleotides window
- Lock oligo list while oligo is open for editing to prevent data written into the wrong place if oligo list is sorted in the meanwhile
- Added "Save as new" to Oligo window
- Oligo list now jumps automatically to newly added oligo
- Cleaned up tab order in Oligo window
- changed "order number" to "delivery number" and "primer order number" to "primer delivery number" to prevent confusion with "PO number"
- Disabled "circular" checkbox as functionality is not yet implemented
- changes to make repeated entries faster and clearer
- "save" button in oligo window stays disabled until data actually change
- squashed a "out of bounds error" when a new oligo was saved into an empty database
Operating System Requirements:
This product is designed to run on the following operating systems:
- Mac OS Classic
Additional Requirements:
- Mac OS 8.5 - 9.2.2
Screenshots:
Download Links:
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Feedback Summary:
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| Overall Rating: | Not rated (0.0) | Features: | Not rated (0.0) | Support: | Not rated (0.0) |
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Commentary 
Featured Reviews
a little anecdote ... - Version: 2.9.5, 2/1/2005 02:33AM PST
MarkusWinter (Markus Winter)
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. :-)
a little anecdote ... - Version: 2.9.5, 2/1/2005 02:33AM PST
MarkusWinter (Markus Winter)
... 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. :-)
After just 3 weeks ... - Version: 2.8, 11/1/2004 04:12AM PST
MarkusWinter (Markus Winter)
I got a total of over 2000 downloads (cumulative total for OligoChecker 2 on MacOS X and MacOS 9 with about 90% on MacOS X). According to Gartner the Mac has a worldwide market share of 1.8% (3.2 in the US) - so I would expect about 20-30 times as many downloads for the Windows version when it becomes available (40,000 – 60,000 (?) ... although 20,000 seems a more realistic total to me). Now if one assumes 20,000 people using the program and saving on average just 15 min a week (not counting other savings), then the cumulative total in saved working hours each week is 5,000 h (the equivalent of 125 full-time positions each year!) ... time which surely could be spend on more interesting research :-)
