btwisted
Function
Description
btwisted takes a region of a pure DNA sequence and calculates
by simple arithmetic the probable overall twist of the sequence and
the stacking energy.
Usage
Command line arguments
Input file format
Nucleic acid sequence USA.
Output file format
Data files
The program reads in two data files.
The first is prompted for by:
"File containing base pair twist angles"
This is the data file 'Eangles.dat' by default.
This consists of the data:
aa 35.6 0.1
ac 34.4 1.3
ag 27.7 1.5
at 31.5 1.1
ca 34.5 0.9
cc 33.7 0.1
cg 29.8 1.1
ct 27.7 1.5
ga 36.9 0.9
gc 40.0 1.2
gg 33.7 0.1
gt 34.4 1.3
ta 36.0 1.0
tc 36.9 0.9
tg 34.5 0.9
tt 35.6 0.1
The second is prompted for by:
"File containing base pair stacking energies"
This is the data file 'Eenergy.dat' by default.
This consists of the data:
#base pair stacking energy for B-DNA
aa -5.37
ac -10.51
ag -6.78
at -6.57
ca -6.57
cc -8.26
cg -9.69
ct -6.78
ga -9.81
gc -14.59
gg -8.26
gt -10.51
ta -3.82
tc -9.81
tg -6.57
tt -5.37
No check is made that all dinucleotides have been read for the energy and
twist. Attempting to run btwisted with an incomplete data file will result
a fatal error if the sequence contains a dinucleotide not in the data files.
Notes
None.
References
None.
Warnings
No check is made that all dinucleotides have been read for the energy
and twist. Attempting to run btwisted with an incomplete data file
will result a fatal error if the sequence contains a dinucleotide not
in the data files.
Diagnostic Error Messages
"Incomplete table"
You have supplied data files for either the angles or energies that do
not contain the fulll required set of possible dinucleotides.
Exit status
It always exits with status 0.
Known bugs
No check is made that all dinucleotides have been read for the energy
and twist. Attempting to run btwisted with an incomplete data file
will result a fatal error if the sequence contains a dinucleotide not
in the data files.
Author(s)
and
This application was written during the first Scandinavian EMBOSS Workshop.
History
Target users
Comments