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CANADA: thermo

thermo (version 1.01)

This program reads DNA sequences and writes some thermodynamic properties to
standard output. These are melting temperature Tm, as well as differences in enthalpy 
Delta H, entropy Delta S, and Gibbs free energy Delta G of the hybridization reaction
between each sequence and its Watson-Crick complement. The sequences are usually
read from an input file. If no filename is given, thermo works in interactive mode. In this
mode the user is prompted to type in a sequence, and the thermodynamic data are put
out immediately. You can leave the interactive mode (and exit the program) by entering @.

See the manual for a more detailed description of this tool.
Read the logfile to see what's new in this version.

Download

The program: thermo.exe (276 KB)
Example input files: example_seqs.txt (1 KB) example_seqs_w_IDs.txt (1 KB)

Examples

With input sequences like these:

ttcgccctgctactaacacg
agataacagcaggatttctt
ggatcgcaggatctcagtca
gtgaccctccttccagtccg
gaattccatatcccttccaa
agaccgggctccgcacctgt
cttcacatacaaaattaatc
gtccttcccgcggtttctac

thermo produces a table like this:

sequence    Tm [deg C]    DeltaH [kcal/mol]    DeltaS [cal/K mol]    DeltaG_37 [kcal/mol]
ttcgccctgctactaacacg    52.3596    -151.4    -405.3    -25.29
agataacagcaggatttctt    43.7015    -141.6    -387.3    -21.58
ggatcgcaggatctcagtca    51.7963    -142.5    -379.6    -24.96
gtgaccctccttccagtccg    57.5841    -141.7    -370.1    -26.51
gaattccatatcccttccaa    44.735    -137.5    -373.5    -21.49
agaccgggctccgcacctgt    62.919    -150.2    -388.2    -29.22
cttcacatacaaaattaatc    37.2746    -143.4    -401.5    -18.77
gtccttcccgcggtttctac    55.496    -150.7    -399.1    -26.37

An interactive session may look like this:

>thermo
Enter sequence (@ to exit):
aaaaaaaaaa
Tm = 1.01574 deg C
DeltaH = -66.5 kcal / mol
DeltaS = -198.622 cal / K per mol
DeltaG = -4.76461 kcal / mol, at 37 deg C

Enter sequence (@ to exit):
gcgcgcgcgc
Tm = 45.7317 deg C
DeltaH = -91.2 kcal / mol
DeltaS = -244.822 cal / K per mol
DeltaG = -15.3446 kcal / mol, at 37 deg C

Enter sequence (@ to exit):
@
last modification: Dec/05/2007

  
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