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                boolean    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:

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 nameDescription
bananaBending and curvature plot in B-DNA
chaosCreate a chaos game representation plot for a sequence
compseqCounts the composition of dimer/trimer/etc words in a sequence
danCalculates DNA RNA/DNA melting temperature
freakResidue/base frequency table or plot
isochorePlots isochores in large DNA sequences
wordcountCounts 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