I use the same numbers as your pattern count. Steven Seeholzer's program
uses up to ten decimal places. Steven's program also recognize spaces and
unrelated values such as 5' and 3' in your input file so that you can
just input your lab notes. The output retains your notes to provide
better bookkeeping. He also allows the indication of 5' and 3' phosphate.
The next version will have programmable keys.
You will notice that none of the sites you referred to below gives the
same numbers as your profile scan will give you. Some are way off for
mass-spectrometry although good enough for molecular biology
applications. If the masses of the oligos used in a standard curve in
two-oligo calibration of MALDI-TOF are off by one proton or more, the
results of the curve extrapolation can be way off. One may erroneously
blame the instrument for not being linear.
You think you will like Steven's program.
Tony
At 06:23 PM 4/24/98 -0700, Martin Pentony wrote:
>>>>
<excerpt>Try these sites. I like the second one but I have no idea how
accurate the calculations are for any of these sites (something I should
check in my free time).
http://paris.chem.yale.edu/extinct.html
http://www.williamstone.com/primers/calculator/
http://www.science.adelaide.edu.au/microb/learn/oligcalc.htm
http://www.user.globalnet.co.uk/~cyk/oligos.html
I also have a molecular weight calculation field in Filemaker Pro as
follows
<fontfamily><param>Geneva</param><bigger><bigger>(PatternCount(Sequence;
"A")* 313.2106) + (PatternCount(Sequence; "G") * 329.21) +
(PatternCount(Sequence; "C") * 289.1854) + (PatternCount(Sequence; "T") *
304.1972) - 61.965
</bigger></bigger></fontfamily>"Sequence" in this calculation is the
reference field where the oligo sequence is entered.
Hope this is what you wanted
Martin Pentony
P.A.N. Facility
Stanford University
>Does someone know of a nice resource (book/reviews or preferably Web
site)
>that has some/all of the following very basic information for common
and
>modified nucleotides found in RNA/DNA:
>
>1. Extinction coefficients - at both 280 and 260 nm - in RNA/DNA
>2. Mono and avg MWs
>3. Simple programs for calculating above for oligos
>
>Thanks very much
>
>
>
>Ken Williams, Ph.D.
>Director, HHMI Biopolymer/Keck Laboratory
>Professor (Adjunct) Research
>Molecular Biophysics and Biochemistry
>
>
>Visit the HHMI Biopolymer/Keck Laboratory Web Page at:
>
> http://info.med.yale.edu/wmkeck/
</excerpt><<<<<<<<
************************************
Dr. Anthony T. Yeung, Ph.D.
Director, Fannie E. Rippel Biotechnology Facility
Member, Institute for Cancer Research
Fox Chase Cancer Center
7701 Burholme Ave. Philadelphia, PA 19111
Voice: 215-728-2488
FAX: 215-728-3647
email: AT_Yeung@FCCC.edu
http://www.fccc.edu/research/labs/yeung/
************************************