banana.txt

emboss的linux版本的源代码

                                  banana 



Function

   Bending and curvature plot in B-DNA

Description

   banana predicts bending of a normal (B) DNA double helix, using the
   method of Goodsell & Dickerson, NAR 1994 11;22(24):5497-5503.

   This program calculates the magnitude of local bending and macroscopic
   curvature at each point along an arbitrary B-DNA sequence, using any
   desired bending model that specifies values of twist, roll and tilt as
   a function of sequence.

   The data, based on the nucleosome positioning data of Satchwell et al
   1986 (J. Mol. Biol. 191, 659-675), correctly predicts experimental
   A-tract curvature as measured by gel retardation and cyclization
   kinetics and successfully predicts curvature in regions containing
   phased GGGCCC sequences. (This is the model 'a' described in the
   Goodsell & Dickerson paper).

   This model - showing local bending at mixed sequence DNA, strong bends
   at the sequence GGC, and straight, rigid A-tracts - is the only model,
   out of six models investigated in Goodsell & Dickerson paper, that is
   consistent with both solution data from gel retardation and
   cyclization kinetics and structural data from x-ray crystallography.

   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 -
   hence the name of this program.

   The program outputs both a graphical display and a text file of the
   results.

  Background

   Sequence-dependent DNA bending, like sequence-dependent prtoein
   folding, is a problem taht remains frustratingly elusive. The issue
   has obvious biological importance in such matters as the winding of
   DNA in nucleosomes, or the recognition of particular DNA loci by
   restriction enzymes, repressors and other control proteins. the
   binding of the catabolite gene activator protein and of the TATA-box
   recognition protein to a double DNA helix are only two spectacular
   examples in which major bends in the helix are induced at specific
   sequence loci. It is of interest to consider whether the particular
   recognition sequences are bent even in the absence of proteins: a
   preformed bend in the DNA would form a custom site for protein
   binding, or an enhanced bendability of a given sequence would
   facilitate protein-induced bending.

   Two possible models of sequence-dependent bending in free DNA have
   been proposed in the past. Nearest neighbor models propose that
   large-scale measurable curvature may arise by the accumulation of many
   small local deformations in helical twist, roll, tilt and slide at
   individual steps between base pairs. junction models, on the other
   hand, propose that bending occurs at the interface between two
   different structural variants of the B-DNA double helix. Note that in
   both of these models, sequences which are anisotropically bendable -
   for instance, sequences with steps that preferentially bend only to
   compress the major groove - will lead to an average structure which is
   similar to a sequence with a rigid, intrinsic bend. The Goodsell &
   Dickerson paper does not distinguish between these two possibilities.

   B-DNA has the special property of having its base pairs very nearly
   perpendicular to the overall helix axis. Hence the normal vector to
   each base pair can be taken as representing the local helix at that
   point, and curvature and bending can be studied simply by observing
   the behaviour of the normal vectors from one base to another along the
   helix. This is both easy to calculate and simple to interpret. This
   program display the magnitude of bending and curvature at each point
   along the sequence. It is not intended as a substitute for more
   elaborate three-dimensional trajectory calculations, but only to
   express bending tendencies as a function of sequence. The power of
   this simple appraoch is in its ease of screening for regions of a
   given DNA sequence where phased local bends add constructively to form
   an overall curve.

   For purposes of clarity the terms bending and curvature will be used
   in a restricted sense here. Bending of DNA describes the tendency for
   successive base pairs to be non-parallel in an additive manner over
   several base pair steps. Bending most commonly is produced by a
   rolling of adjacent base pairs over one another about thir long axis,
   although in principle, tilting of base pairs about their short axis
   could make a contribution. In contrast curvature of DNA represents the
   tendency of the helix axis to follow a non-linear pathway over an
   appreciable length, in a manner that contributes to macroscopic
   behaviour such as gel retardation or ease of cyclization into DNA
   minicircles. The distinction between local bending and macroscopic
   curvature is illustrated (poorly) in the following figure (see figure
   1 of the Goodsell & Dickerson paper for a better view).

                       bend   bend   bend
                         -     -     -
  uncurved              / \   / \   / \
                  -----/   \-/   \-/   \-----
                          bend   bend




                    bend    bend
                     /-------\
                   /          \
  curved          |bend        |bend
                  |            |
                  |            |


   An x-ray crystal structure analysis cannot show curvature, but can and
   often does show local bending. On the other hand gel electrophoresis
   and cyclization kinetics can detect macroscopic curvature, but not
   bending. A complete knowledge of local bending would permit the
   precise calculation of curvature, but a knowledge of macroscopic
   curvature alone does not allow one to specify precisely the local
   bending elements that produce it. This is one of the scale paradoxes
   that have plagued the DNA conformation field for a decade or more.
   There is more than a passing resemblence to a familiar problem of
   classical statistical mechanics: A complete knowledge of instantaneous
   positions and velocities of all molecules of a gas allows one to
   calculate bulk properties such as temprature, pressure and volume. But
   the most detailed knowledge of bulk properties cannot lead one to
   precise molecular positions. Many molecular arrangements can produce
   identical bulk properties, and in the present case, many bending
   combinations can produce identical macroscopic curvature.

  Method

   The program reads a sequence and a matrix of standard twist, roll and
   tilt angles for each type of base pair step. This matrix is entirely
   at the disposal of the user, and can be altered to represent any other
   DNA-bending model. The program creates a table or a graphical image of
   the bending and the curvature at each base step.

   The program begins by applying the indicated twist, roll and tilt at
   each step along the sequence, and calculating the resulting base pair
   normal vector. The first base pair is aligned normal to the z axis,
   with a twist value of 0.0 degrees. the specified twist is applied to
   the second base pair, and roll and tilt values are use dto calculate
   its normal vector relative to the first. If either roll or tilt is
   non-zero, the new normal vector will be angled away from the z axis,
   producing the first 'bend'. the process is continued along the
   sequence, applying the appropriate twist, roll and tilt to each new
   base pair relative to its predecessor. The result is a list of normal
   vectors for all base pairs in the sequence.

   Local bends are then calculated from the normal vectors. The bend for
   base N is calculated across a window from N-1 to N+1.

   Curvature is calculated in two steps. Base pair normals are first
   averaged over a 10-base-pair window to filter out the local writhing
   of the helix. The normals of the nine base pairs from N-4 to N+4, and
   the two base pairs N-5 and N+5 at half weight, are averaged and
   assigned to base pair N. Curvature then is calculated from these
   averaged normal vector values, using a bracket value, nc, with a value
   of 15. That is, the curvature at base pair N is the angle between
   averaged normal vectors at base pairs N-nc and N+nc.

Usage

   Here is a sample session with banana


% banana -nooutfile -graph ps 
Bending and curvature plot in B-DNA
Input nucleotide sequence: tembl:rnu68037

Created banana.ps

   Go to the input files for this example
   Go to the output files for this example

   Example 2


% banana -graph data 
Bending and curvature plot in B-DNA
Input nucleotide sequence: tembl:rnu68037

Created banana1.dat
Created banana2.dat
Created banana3.dat
Created banana4.dat
Created banana5.dat
Created banana6.dat
Created banana7.dat
Created banana8.dat
Created banana9.dat

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
   -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png)

   Additional (Optional) qualifiers:
   -anglesfile         datafile   [Eangles_tri.dat] DNA base timer roll angles
                                  data file
   -residuesperline    integer    [50] Number of residues to be displayed on
                                  each line (Any integer value)
   -outfile            outfile    [banana.profile] Output file name

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages