[EMBOSS] Question about DeltaS and DeltaH
Bassi, Sebastian
sebastian.bassi at ar.advantaseeds.com
Thu Nov 27 03:08:55 UTC 2003
Hello,
I'm trying to reproduce the DeltaS and deltaH results from dan.c in Python (in order to add tm as a function in BioPython). But I found some differences in dan's DeltaS calculation and my own calculations.
I tried to follow EMBOSS code (dan.c, ajdan.c, Edna.melt) but I am not an C expert (just a newbie) so I can't follow all the code.
I will tell you what I'm doing, maybe somebody could point me out my mistake.
To get DeltaS (entropy) I'm adding all the ocurrences of all neighbor pair secuences:
Take this sequence: ACCCTTCAGCAGTTCCACAC
Here are all neighbors and their DeltaS values:
AC = 22.4
CC = 19.9
CT = 21
TT = 22.2
TC = 22.2
CA = 22.7
AG = 21
GC = 24.4
CA = 22.7
AG = 21
GT = 22.4
TT = 22.2
TC = 22.2
CC = 19.9
CA = 22.7
AC = 22.4
CA = 22.7
AC = 22.4
Grant total = 396.4
According to DAN, the result should be:
416.3
It seems there is something I'm missing. Could you please give me a hint about this?
Sebastian Bassi.
Advanta Seeds. Balcarce Research Station.
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