EMBOSS: banana


Program banana

Function

Bending and curvature plot in B-DNA

Description

Banana predicts bending of a normal (B) DNA double helix.

The consensus sequence for DNA bending is 5 As and 5 non-As alternating. "N" is an ambiguity code for any base, and "B" is the ambiguity code for "not A" so "BANANA" is itself a bent sequence.

Usage

Here is a sample session with banana.

 banana embl:rnu68037

click here for result (1st page only)

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
*  -graph              graph      Graph type

   Optional qualifiers:
   -anglesfile         datafile   angles file
   -residuesperline    integer    Number of residues to be displayed on each
                                  line
   -outfile            outfile    Output file name

   Advanced qualifiers:
   -data               bool       Output as data


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm EMBOSS_GRAPHICS value, or x11
Optional qualifiers Allowed values Default
-anglesfile angles file Data file Eangles_tri.dat
-residuesperline Number of residues to be displayed on each line Any integer value 50
-outfile Output file name Output file banana.profile
Advanced qualifiers Allowed values Default
-data Output as data Yes/No No

Input file format

Any DNA sequence USA.

Output file format

.ps file if postscipt output requested.

Data files

angles files. By default Eangles_tri.dat is used.

Notes

References

Goodsell, D.S. & Dickerson, R.E. (1994) "Bending and Curvature Calculations in B-DNA" Nucl. Acids. Res. 22, 5497-5503.

Warnings

Only ACTG allowed, if sequence contains a non ACTG character then the program will exit with a fatal error message.

Diagnostic Error Messages

Exit status

0 if successfull.

Known bugs

See also

Program nameDescription
btwistedCalculates the twisting in a B-DNA sequence
complexFind the linguistic complexity in nucleotide sequences
danCalculates DNA RNA/DNA melting temperature

Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Created 1999/06/09.
Last Updated 1999/06/14.

Target users

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

Comments