OligoCalc V 1.04 (June 17th, 1998)

This program is my first attempt to make an application for Palm Pilot.
It is freeware. I wrote if for molecular biologists who have to deal with 
oligonucleotide synthesis and purification. Actually, I am one of them:)


                      Update information
v 1.04 (06.17.98) size 8k
The sequence of the last entered oligonucleotide is displayed after 
reopening OligoCalc. 

v 1.03 (05.31.98) size 7k
A new menu item "Export to Clipboard" has been added. It puts the
sequence of the oligonucleotide and its calculated parameters into the 
clipboard.
The program can recognize lower case letters now. 
If a sequence is longer than 100 letters the program gives an error 
message instead of crashing.


v 1.02 (05.25.98) size 6k
Now you can paste an oligonucleotide sequence from the clipboard.
In help-info an oligonucleotide optimum melting temperature 
for PCR is corrected.
Zip file includes the source of OligoCalc. 

v 1.01 (05.12.98) size 6k
 A bug was fixed that crashed the program when 
oligonucleotides without C or G were entered.

v1.00 (05.11.95) size 6k
First release

                         Description

Here is a list of all the formulas I used for the calculations. The problem is
that different companies, programs and persons use slightly different 
constants for calculating the extinction coefficient and molecular weight. If
you want have your coefficients in the formulas really badly, write me a 
letter. I hope I'll find 10 minutes to change them in the source code and to
recompile it for you. I think after 5 or ten letters I'll have the most 
popular variants. 

Also, if you use GCC Palm Pilot SDK you can modify a source code and then recompile the 
program again (you need to start included compile.bat for that)
All extinction coefficients are defined at lines 38-41 (oligo.c file).  


Here are the formulas I used for calculations:

1) Molar Extinction coefficient

Ext=(#A*15300)+(#C*7400)+(#G*11800)+(#T*9300)

2) Molecular Weight (Ammonium salt) (Da)

MW=(((#A*313.2)+(#C*289.2)+(#G*329.2)+(#T*304.2))-62)+((Number of bases-1)*17)

3) Length (bases)

Len=Number of bases

4) Melting temperature calculated for 1M NaCl solutions (Celsius degrees)

Tm C=81.5+0.41(GC%)-(675/Length)

5) GC%

GC%=(#G+#CC)/Length *100

6) One Optical Density Unit at 260 nm is nmol/ml

1O.D.(nmol)=1,000,000/Ext

7) One Optical Density Unit at 260nm is ug/ml

1 O.D.(ug)=MW*1000/Ext





To contact me - write an e-mail to dimus_m@hotmail.com

Dmitry Mozzherin

May 9th, 1998