Thursday, February 21, 2008

NucProt Calculator Error in RNA Analysis

I was trying to use the program NucProt calculator for an RNA sequence of 7.4 kB. I always get an error message instead of an answer. What is the maximum length sequence allowed as input in the program.

It is actually a quite simple script. It only counts how many A, C, G, Us there are and uses the formula:
"Exact" calculation
volume (cubic Angstroms) = #A*315.45 + #C*291.285 + #G*323.028 + #U*291.285
mass (Daltons) = #A*329.2 + #C*305.2 + #G*345.2 + #U*306.2

For an RNA that size the average might just as good:
7.4kB * 304 A^3 ~= 2.25 million cubic Angstroms
7.4kB * 321.45 A^3 ~= 2.38 MD (MegaDaltons)
PSV is something like volume/mass*0.6022 ~= 0.57


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