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Re: how to make this code more efficient? Need to Compute the Min and Max of a Temperature using an equation

by MadraghRua (Vicar)
on Apr 20, 2010 at 18:25 UTC ( #835851=note: print w/ replies, xml ) Need Help??


in reply to how to make this code more efficient? Need to Compute the Min and Max of a Temperature using an equation

Treat it less as a brute force challenge and think about your data. You have a sting
NNYDBAVDVHVHNGGNR

What parameters will increase the Tm? - C and G residues
What parameters will decrease the Tm? - A and T residues

For each residue, find if IUPAC can give you a C or a G for the max temperature at that residue, then a T or an A for the min temperature.

If you really need to calculate over large numbers of primers then divide the primers up into percentiles, eg 90% GC, 80% GC and so on. Its an approximation but good enough for what I think you are doing.

If you need more accuracy yet, look at your hash values - this shows you the residue pairs that give you most and least values, so see waht pairs of residues are likely for the extremes of these values and bias the calculations to those primers

Just out of curiosity where are you getting the enthalpy and entrophy values from? St. Lucia?

One other thought - if you want accurate temps, you're going to want to calculate on the monovalent and divalent ion concentrations. I suggest looking at Primer 3 for ways to calculate these values. Or simply call Primer3 rather than reinventing this in your app - it gives this information anyway.

Good luck

MadraghRua
yet another biologist hacking perl....


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