Version history for Oligonucleotide Properties Calculator
Current version is available at http://www.basic.northwestern.edu/biotools/OligoCalc.html
Version 1.0 04/15/97 wakibbe Created Oligo Calc with Thermodynamic and two empirical Tm calculations released
Version 1.1 ???????? wakibbe Added BLAST2 submission feature
Version 1.2 ???????? wakibbe Added fluorescent tag calculations, 'Swap Strands' feature.
Version 1.3 ???????? wakibbe Added hairpin formation feature
Version 2.0 10/25/99 Qing Cao Changed Blast2, linked to the new NLM NCBI site. (Old site was http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-newblast, new site is: http://www.ncbi.nlm.nih.gov/blast/blast.cgi
Version 2.01 05/2000 Qing Cao Added self-complementarity calculation
Version 2.01 08/2000 Qing Cao Disabled hairpin calculation for IE 4. hairpin calc only for Netscape [works for IE 5 and higher].
Version 3.01 12/19/2000 wakibbe bug fixes for IE
Version 3.02 02/23/2002 wakibbe complement calculation bug described by Alexey Merz email@example.com resolved
Version 3.03 02/09/2004 wakibbe Added compatibility features for Safari and Mozilla browsers
Version 3.04 02/12/2004 wakibbe Changed BLAST configuration yet again
Version 3.05 02/13/2004 wakibbe Changed MW to add a monophosphate vs subtract a pyrophosphate (add 79.0 gm/mol instead of subtracting 61.96)
Version 3.06 02/14/2004 wakibbe Added ssDNA/dsDNA/ssRNA/dsRNA options
Version 3.07 03/26/2004 wakibbe Moved MW calculation back to the old method, and added notes in the MW formula area. Also changed links to the paper abstracts to new NCBI urls, added RNA thermodynamics paper to references.
Version 3.08 07/01/2004 wakibbe Changed the fluorescent tags to accept 5' and 3' tags. Added many new fluorescent tags to the lists. Changed the way the fluorescent tags MW were calculated. Massive changes to the look of the calculator. I wonder if anyone will comment? Moved the concentrations of primer and salt up into the area for user input.
Version 3.09 07/18/2006 wakibbe Clarified discussion of when the various equations are actually used.
Version 3.10 09/25/2006 wakibbe Fixed double-stranded molecular weight calcuation error identified by Borries Demeler. Thanks Borries!
Version 3.11 01/10/2007 wakibbe Added note and citation about divalent cations. Added link to source code download
Version 3.12 01/28/2007 wakibbe Corrected 'flourescent' typo, added additional references for basic and salt adjusted calculations for RNA.
Version 3.13 01/29/2007 wakibbe Corrected a long standing bug in the hairpin/complementarity code, where the IUPAC code 'M' was not being properly calculated. Reported by Paul Wayper in March of 2005. Sorry Paul for not making the patch available sooner! Submitted OligoCalc manuscript to webserver edition of NAR. Only about seven years later than I should have submitted it.
Version 3.14 03/19/2007 wakibbe Moved Usage Patterns writeup out of NAR manuscript into its own page (http://www.basic.northwestern.edu/biotools/OligoCalcUsage.html) and added stylesheets for this page, Usage Patterns page.
Version 3.15 03/20/2007 wakibbe Moved the Absorbance entry item up into the entry area to make it more obvious. Removed the hairpin and complementarity selections.
Version 3.16 03/21/2007 wakibbe Replaced the old 'Self-Complementarity Check' code with a call to the mfold server at RPI.
Version 3.17 03/21/2007 wakibbe Rewrote BLAST code to either pull data from the 'opener' code or from a cookie.
Version 3.18 03/21/2007 wakibbe Made the BLAST window code and the mfold calling window code very similar, pulled some functions into their own file. Cookies are not working with Safari. Works fine with Mozilla, IE, FireFox, Camino. Why is there always one browser that makes it difficult, and why is it never the same browser?
Version 3.19 03/22/2007 wakibbe Yike! Lots of complaints! Added the old check back, kept the code with a call to the mfold server at RPI.
Version 3.20 04/26/2007 wakibbe Removed all the meta tags and duplicate version info from the main OligoCalc page, changed title and two of the documentation titles.
Version 3.21 07/04/2007 wakibbe Added Nucleic Acids Research citation, cleaned up and removed some details, cleaned up the contact info and thank you section at the end of the main page, and corrected a citation typo (changed Proc. Nuclec Acids Res. to Nucleic Acids Res.).
Version 3.22 03/12/2008 wakibbe Corrected long standing OD calculation error brought to my attention by Rachel Mitton-Fry at Yale.
Version 3.23 05/15/2008 wakibbe Changed the m-fold URL to the latest URL used by Michael Zuker's m-fold web server. Brought to my attention by Jeremy Edwards at the University of New Mexico Health Sciences Center.
Version 3.24 01/17/2009 wakibbe Added link to Russian lnguage version of Oligocalc maintained by Leonid Valentovich.
Version 3.25 07/23/2009 wakibbe Corrected another longstanding failure to include A260s for 3' and 5' modifications in the OD calculations. Reported by Kate Lieberman at the University of California, Santa Cruz.
Version 3.26 07/15/2010 wakibbe Added a feature to include 0.01 degree accuracy for SNP study oligos based on a request from Dr. Zhao Chen at MD Anderson. He had glowing things to say. I quote:
Hi Dr. Kibbe, I tried to use the software OligoCalc to calculate the Tm values of the amplicon of High Resolution Melting assay. It worked perfectly, especially through the Nearest Neighbor method, which exactly matched the experimental value by the LightCycler machine from Roche. But the issue is that since HRM is looking at gene mutations of 1 single base pair in most of the cases. So the changes in Tm are very small, normally less than 1 degree. But your software can not provide values in the format of 80.XX. So all the mutations will have same Tm. I think it's best I ever tried.But I hope this software can improve the resolution and this will make it usable for HRM analysis. Thanks a lot! -------------------------------------------------------------------------- Zhao Chen Ph.D. Molecular Diagnostic Laboratory Department of Hematopathology MD Anderson Cancer Center. Box 149 University of Texas Health Science Center at Houston 8515 Fannin, NAO1.061a Houston, TX 77054
Thank you Dr. Chen!