
                              EMBOSS: btwisted
     _________________________________________________________________
   
                               Program btwisted
                                       
Function

   Calculates the twisting in a B-DNA sequence
   
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

   Here is a sample session with btwisted:

% btwisted embl:ab000095 -sbegin 100 -send 120
Calculates the twisting in a B-DNA sequence
Output file [ab000095.btwisted]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -angledata          string     File containing base pair twist angles
   -energydata         string     File containing base pair stacking energies

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.btwisted
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -angledata File containing base pair twist angles Any string is
   accepted Eangles.dat
   -energydata File containing base pair stacking energies Any string is
   accepted Eenergy.dat
   
Input file format

   Nucleic acid sequence USA.
   
Output file format

   This is the output from the example usage above:
   
# Output from BTWISTED
# Twisting calculated from 100 to 120 of AB000095
Total twist (degrees): 646.6
Total turns : 1.80
Average bases per turn: 11.69
Total stacking energy : -172.77
Average stacking energy per dinucleotide: -8.64

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.
   
   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.
   
   To see the available EMBOSS data files, run:
   
% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".
   
   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata
       
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.
   
See also

   Program name                          Description
   banana       Bending and curvature plot in B-DNA
   chaos        Create a chaos game representation plot for a sequence
   compseq      Counts the composition of dimer/trimer/etc words in a sequence
   dan          Calculates DNA RNA/DNA melting temperature
   freak        Residue/base frequency table or plot
   isochore     Plots isochores in large DNA sequences
   wordcount    Counts words of a specified size in a DNA sequence
   
Author(s)

   This application was written by David Martin (dmartin@hgmp.mrc.ac.uk)
   and Alan Bleasby (ableasby@hgmp.mrc.ac.uk) during the first
   Scandinavian EMBOSS Workshop.
   
History

   Written (Sept 2000) - David Martin & Alan Bleasby.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
