Function

Description

btwisted reads 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

Output file format

Data files

The program requires two data files. A file (Eangles.dat by default) containing base pair twist angles, and another (Eenergy.dat) containing base pair stacking energies. No check is made that all dinucleotides are listed in the files and so read for their 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.

Eangles.dat 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

'Eenergy.dat' 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

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

This application was written during the first Scandinavian EMBOSS Workshop.

History

Target users

Comments