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