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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: banana
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
banana
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Plot bending and curvature data for B-DNA

<H2>
    Description
</H2>

<p><b>banana</b> predicts bending of a normal (B) DNA double helix,
using the method of Goodsell & Dickerson, NAR 1994
11;22(24):5497-5503.  The 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 program
outputs both a graphical display and a text file of the results.</p>

<p>The default model (model 'a' from the Goodsell & Dickerson paper)
is based on the nucleosome positioning data of Satchwell et al 1986
(J. Mol. Biol. 191, 659-675).  It correctly predicts experimental
A-tract curvature as measured by gel retardation and cyclization
kinetics and successfully predicts curvature in regions containing
phased <tt>GGGCCC</tt> sequences. The model shows local bending at
mixed sequence DNA, strong bends at the sequence <tt>GGC</tt>, and
straight, rigid A-tracts.  It is the only model out of the six
investigated that is consistent with both solution data from gel
retardation and cyclization kinetics and structural data from x-ray
crystallography.</p>


<H2>
     Algorithm
</H2>
<p><b>banana</b> reads a sequence and a matrix of standard twist, roll
and tilt angles for each type of base pair step. The default matrix is
described below (see "Bending Model") but some other can be specified
(see "Data Files" below).  The program creates a table or a graphical
image of the bending and the curvature at each base step.</p>

<p>The indicated twist, roll and tilt angles are applied at each step
along the sequence, and the resulting base pair normal vector
calculated. 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 to 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.</p>

<p>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.</p>

<p>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.</p>


<h3>Bending Model</h3>
<p><b>banana</b> reads by default a data file (Eangles_tri.dat) of
twist, roll and tilt angles, as in Goodsell & Dickerson, NAR 1994
11;22(24):5497-503 and Drew and Travers (1986) JMB 191, 659.  The
roll-tilt-twist parameters of this bending model are objective and
unbiased.  They are derived purely from experimental observations of
sequence location preferences of base trimers in small circles of DNA,
without reference to solution techniques that measure curvature per
se.</p>

<p>Satchwell, Drew and Travers studied the positioning of DNA
sequences wrappped around nucleosome cores, and in closed circles of
double-helical DNA of comparable size. From the sequence data they
calculated a fractional preference of each base pair triplet for a
position 'facing out', or with the major groove on the concave side of
the curved helix.</p>
<p>The sequence GGC, for example, has a 45% preference for locations
on a bent double helix in which its major groove faces inward and is
compressed by the curvature (tending towards positive roll), whereas
sequence AAA has a 36% preference for the opposite orientation, with
major groove facing outward and with minor groove facing inward and
compressed (tending toward negative roll).</p>
<p>These fractional variances are converted into roll angles in the
following manner: Because x-ray cyrstal structure analysis uniformly
indicates that AA steps are unbent, a zero roll is assigned to the AAA
triplet; an arbitrary maximum roll of 10 degrees is asigned to GGC,
and all other triplets are scaled in a lenear manner. Where % is the
percent-out figure, then:

         Roll = 10 degrees * (% + 36)/(45 + 36)
</p>

<p>Changing the maximum roll value will scale the entire profile up or
down proportionately, but will not change the shape of the
profile. Peaks will remain peaks, and valleys, valleys. The absolute
magnitude of all the roll values is less important than their relative
magnitude, or the order of roll preference. Twist angles were set to
zero. Because these values correspond to base trimers, the values of
roll, tilt and twist were applied to the first two bases for the
calculation.</p>





<H2>
    Usage
</H2>
Here is a sample session with <b>banana</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>banana -nooutfile -graph ps </b>
Plot bending and curvature data for B-DNA
Input nucleotide sequence: <b>tembl:u68037</b>

Created banana.ps

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>banana -graph data </b>
Plot bending and curvature data for B-DNA
Input nucleotide sequence: <b>tembl:u68037</b>

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

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Plot bending and curvature data for B-DNA
Version: EMBOSS:6.6.0.0

   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,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)

   Additional (Optional) qualifiers:
   -anglesfile         datafile   [Eangles_tri.dat] DNA base trimer 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>sequence</td>
<td>Nucleotide sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-graph</td>
<td>graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-anglesfile</td>
<td>datafile</td>
<td>DNA base trimer roll angles data file</td>
<td>Data file</td>
<td>Eangles_tri.dat</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-residuesperline</td>
<td>integer</td>
<td>Number of residues to be displayed on each line</td>
<td>Any integer value</td>
<td>50</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td>banana.profile</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated sequence qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-graph" associated graph qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gprompt</td>
<td>boolean</td>
<td>Graph prompting</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gdesc</td>
<td>string</td>
<td>Graph description</td>
<td>Any string</td>
<td>Bending and curvature plot</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gtitle</td>
<td>string</td>
<td>Graph title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gsubtitle</td>
<td>string</td>
<td>Graph subtitle</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gxtitle</td>
<td>string</td>
<td>Graph x axis title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gytitle</td>
<td>string</td>
<td>Graph y axis title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -goutfile</td>
<td>string</td>
<td>Output file for non interactive displays</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gdirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<H2>
    Input file format
</H2>

<b>banana</b> reads a single nucleotide sequences.

<p>
<p>

The output is a standard EMBOSS sequence file. 

<p>

The results can be output in one of several styles by using the
command-line qualifier <tt>-osformat xxx</tt>, where 'xxx' is replaced by
the name of the required format.  The available format names are: embl,
genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel,
feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>

<p>

<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tembl:u68037' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:u68037</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   U68037; SV 1; linear; mRNA; STD; ROD; 1218 BP.
XX
AC   U68037;
XX
DT   23-SEP-1996 (Rel. 49, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 2)
XX
DE   Rattus norvegicus EP1 prostanoid receptor mRNA, complete cds.
XX
KW   .
XX
OS   Rattus norvegicus (Norway rat)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   Muridae; Murinae; Rattus.
XX
RN   [1]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   "Cloning of the rat EP1 prostanoid receptor";
RL   Unpublished.
XX
RN   [2]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   ;
RL   Submitted (26-AUG-1996) to the INSDC.
RL   Biochemistry &amp; Molecular Biology, Merck Frosst Center for Therapeutic
RL   Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada
XX
DR   Ensembl-GO; ENSRNOESTG00000830631; Rattus_norvegicus.
DR   Ensembl-Gn; ENSRNOG00000004094; Rattus_norvegicus.
DR   Ensembl-Gn; ENSRNOG00000017743; Rattus_norvegicus.
DR   Ensembl-TO; ENSRNOESTT00000830623; Rattus_norvegicus.
DR   Ensembl-Tr; ENSRNOT00000005470; Rattus_norvegicus.
DR   Ensembl-Tr; ENSRNOT00000023860; Rattus_norvegicus.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1218
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:10116"
FT   CDS             1..1218
FT                   /codon_start=1
FT                   /product="EP1 prostanoid receptor"
FT                   /note="family 1 G-protein coupled receptor"
FT                   /db_xref="GOA:P70597"
FT                   /db_xref="InterPro:IPR000276"
FT                   /db_xref="InterPro:IPR000708"
FT                   /db_xref="InterPro:IPR001244"
FT                   /db_xref="InterPro:IPR008365"
FT                   /db_xref="InterPro:IPR017452"
FT                   /db_xref="UniProtKB/Swiss-Prot:P70597"
FT                   /protein_id="AAB07735.1"
FT                   /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFSM
FT                   TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTAG
FT                   RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALALL
FT                   AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAALV
FT                   CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALRS
FT                   SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLAV
FT                   RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSRH
FT                   SGFSHL"
XX
SQ   Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
     atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc        60
     agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg       120
     cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc       180
     caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc       240
     agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg       300
     tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc       360
     ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt       420
     gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta       480
     gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac       540
     tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg       600
     cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca       660
     ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc       720
     tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga       780
     ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc       840
     agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc       900
     cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg       960
     gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta      1020
     cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct      1080
     atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg      1140
     gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt      1200
     ggcttcagcc acttgtga                                                    1218
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

The output is to both a graphical display and to a text file with the
default name 'banana.profile'.

<p>

The graphical display shows the sequence together with the local local
bending (solid line) and macroscopic curvature (dotted line). 

<p>
<p>

The output is to the specified graphics device.

<p>

The results can be output in one of several formats by using the
command-line qualifier <b>-graph xxx</b>, where 'xxx' is replaced by
the name of the required device. Support depends on the availability
of third-party software packages.

<p>
The device names that output to a file are:
ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470,
hp7580, das, data.

<p> The other available device names are: meta, x11 (xwindows), tek
(tek4107t), tekt (tektronix), xterm, text.

<p>
Output can be turned off by specifying none (null).

<p>

See:
<A href="http://emboss.sf.net/docs/themes/GraphicsDevices.html">
http://emboss.sf.net/docs/themes/GraphicsDevices.html</A>
for further information on supported devices.

<p>
<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Graphics File: banana.ps</h3>
<p><img src="banana.1.banana.gif" alt="[banana results]">

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: banana.profile</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Base   Bend      Curve
a       0.0      0.0
t      19.7      0.0
g      17.7      0.0
a      21.1      0.0
g      28.5      0.0
c      26.2      0.0
c      19.7      0.0
c      18.7      0.0
c      12.5      0.0
t       9.7      0.0
a      14.9      0.0
c      16.5      0.0
g      17.5      0.0
g      26.2      0.0
g      28.5      0.0
c      20.7      0.0
t      11.7      0.0
t       6.4      0.0
a       9.3      0.0
a      14.9      0.0
c      17.7     20.0
c      15.7     19.2
t      15.7     18.5
g      17.7     17.9
a      21.1     17.1
g      28.5     15.9
c      25.2     14.6
c      12.5     13.3
t       7.2     11.9
a      13.2     10.8
g      20.1     10.1
t      19.5      9.6
g      15.1      9.2
g      14.9      9.1
a      19.5      9.5
t      19.7     10.2
g      17.7     10.8
a      17.7     11.0
g      25.2     11.2
g      26.2     11.3
c      15.3     11.5
a      11.4     11.7
a      14.5     12.0
c      13.9     12.2
a      11.4     12.3
a      14.9     12.5
c      17.7     12.8
g      19.5     13.3
t      19.1     13.5


<font color=red>  [Part of this file has been deleted for brevity]</font>

g      15.1     15.2
a      17.7     15.5
g      25.2     15.8
g      32.5     16.0
c      25.2     15.8
c      15.7     15.0
a      16.3     14.2
g      15.5     13.5
t      10.8     12.8
t      13.7     12.3
c      19.5     12.1
a      20.1     12.1
c      16.3     12.1
t      16.7     11.9
g      22.1     11.4
c      21.1     11.1
g      14.9     10.7
t       9.7     10.3
a      16.1      9.8
g      24.5      9.4
c      21.1      8.9
t      15.1      8.4
c      16.1      7.7
c      17.5      7.3
c      15.3      6.9
g      24.0      6.4
g      26.2      5.8
c      20.5      5.4
a      19.1      5.1
c      15.3     26.0
a      16.3      0.0
g      20.1      0.0
t      19.5      0.0
g      25.2      0.0
g      28.5      0.0
c      20.7      0.0
t      13.3      0.0
t      13.7      0.0
c      15.7      0.0
a      19.1      0.0
g      28.5      0.0
c      25.2      0.0
c      19.5      0.0
a      20.1      0.0
c      17.9      0.0
t      13.9      0.0
t      13.9      0.0
g      19.1      0.0
t      19.5      0.0
g       0.0      0.0
a       0.0      0.0
</pre>
</td></tr></table><p>
<p><h3>File: banana1.dat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##Maintitle Bending and curvature plot of tembl-id:U68037
##Subtitle Mon 15 Jul 2013 12:00:00
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</pre>
</td></tr></table><p>
<p><h3>File: banana2.dat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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<p><h3>File: banana3.dat</h3>
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<p><h3>File: banana4.dat</h3>
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<p><h3>File: banana5.dat</h3>
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<p><h3>File: banana6.dat</h3>
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<p><h3>File: banana7.dat</h3>
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<p><h3>File: banana8.dat</h3>
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</td></tr></table><p>
<p><h3>File: banana9.dat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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</pre>
</td></tr></table><p>
<p>

The data file consists of three columns separated by blanks or tab
characters. 

<p>

The first column is the sequence.  
<br> 
The second column is the local bending.
<br>
The third is the curvature. 


<H2>
    Data files
</H2>

<b>banana</b> requires a data file in the EMBOSS data directory
containing the twist, roll and tilt angles. By
default <tt>Eangles_tri.dat</tt> is used, as in Goodsell & Dickerson,
NAR 1994 11;22(24):5497-503 and Drew and Travers (1986) JMB 191, 659.
Some other file may be specified with the <tt>-anglesfile</tt> option.



<p>

The description of this bending model is as follows:

<p>

The roll-tilt-twist parameters of this model are derived purely from
experimental observations of sequence location preferences of base
trimers in small circles of DNA, without reference to solution
techniques that measure curvature <i>per se</i>.  For this reason,
they may be the most objective and unbiased parameters of all.
Satchwell, Drew and Travers studied the positioning of DNA sequences
wrappped around nucleosome cores, and in closed circles of
double-helical DNA of comparable size.  From the sequence data they
calculated a fractional preference of each base pair triplet for a
position 'facing out', or with the major groove on the concave side of
the curved helix.  The sequence GGC, for example, has a 45% preference
for locations on a bent double helix in which its major groove faces
inward and is compressed by the curvature (tending towards positive
roll), whereas sequence AAA has a 36% preference for the opposite
orientation, with major groove facing outward and with minor groove
facing inward and compressed (tending toward negative roll).  These
fractional variances have been converted into roll angles in the
following manner: Because x-ray cyrstal structure analysis uniformly
indicates that AA steps are unbent, a zero roll is assigned to the AAA
triplet; an arbitrary maximum roll of 10 degrees is asigned to GGC,
and all other triplets are scaled in a lenear manner.  Where % is the
percent-out figure, then:

<p>

<pre>
         Roll = 10 degrees * (% + 36)/(45 + 36)
</pre>

<p>

Changing the maximum roll value will scale the entire profile up or
down proportionately, but will not change the shape of the profile.
Peaks will remain peaks, and valleys, valleys.  The absolute magnitide
of all the roll values is less important than their relative
magnitude, or the order of roll preference.  Twist angles were set to
zero.  Because these values correspond to base trimers, the values of
roll, tilt and twist were applied to the first two bases for the
calculation.



<H2>
    Notes
</H2>

<p>DNA bending is vital for the winding of DNA in nucleosomes, and the
recognition of particular DNA loci by restriction enzymes, repressors
and other control proteins. For example, the binding of the catabolite
gene activator protein and of the TATA-box recognition protein to a
double DNA helix both rely on major bends in the helix induced at
specific sequence loci. Whether the particular recognition sequences
are bent even in the absence of proteins is not always clear: 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. Sadly, the rules of
sequence-dependent DNA bending remain elusive.</p>

<p>Two models of sequence-dependent bending in free DNA have been
proposed. 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. In contrast, junction models propose that
bending occurs at the interface between two different structural
variants of the B-DNA double helix.</p>
<p>In both 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 default
bending model (see below) used by <b>banana</b> does not distinguish
between these two possibilities.</p>

<p>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. This affords
easy screening for regions of a given DNA sequence where phased local
bends add constructively to form an overall curve.</p>

<p>The terms bending and curvature are 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.</p>

<p>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).</p>


<pre>
                       bend   bend   bend
                         -     -     -
  uncurved              / \   / \   / \
                  -----/   \-/   \-/   \-----
                          bend   bend
                  


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


</pre>

<p>X-ray crystal structure analysis cannot show curvature, but can and
often does show local bending. Conversely, 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 paradox has plagued the DNA
conformation field resembles the familiar problem of classical
statistical mechanics, where a complete knowledge of positions and
velocities of all molecules of a gas would allow one to calculate bulk
properties such as temperature, pressure and volume, but 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.</p>

<p>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.</p>


<H2>
    References
</H2>

<ol>

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

<li>Drew and
Travers (1986) JMB 191, 659

</ol>

<H2>
    Warnings
</H2>

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

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

    0 if successful.

<H2>
    Known bugs
</H2>

None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="btwisted.html">btwisted</a></td>
<td>Calculate the twisting in a B-DNA sequence</td>
</tr>

<tr>
<td><a href="chaos.html">chaos</a></td>
<td>Draw a chaos game representation plot for a nucleotide sequence</td>
</tr>

<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Calculate the composition of unique words in sequences</td>
</tr>

<tr>
<td><a href="dan.html">dan</a></td>
<td>Calculate nucleic acid melting temperature</td>
</tr>

<tr>
<td><a href="density.html">density</a></td>
<td>Draw a nucleic acid density plot</td>
</tr>

<tr>
<td><a href="einverted.html">einverted</a></td>
<td>Find inverted repeats in nucleotide sequences</td>
</tr>

<tr>
<td><a href="freak.html">freak</a></td>
<td>Generate residue/base frequency table or plot</td>
</tr>

<tr>
<td><a href="isochore.html">isochore</a></td>
<td>Plot isochores in DNA sequences</td>
</tr>

<tr>
<td><a href="sirna.html">sirna</a></td>
<td>Find siRNA duplexes in mRNA</td>
</tr>

<tr>
<td><a href="wordcount.html">wordcount</a></td>
<td>Count and extract unique words in molecular sequence(s)</td>
</tr>

</table>

<H2>
    Author(s)
</H2>


Ian Longden formerly at:
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.                      

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.


<H2>
    History
</H2>

The original program ('BEND') is described in the Goodsell & Dickerson paper.

Created 1999/06/09.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.


<H2>
    Comments
</H2>
None

</BODY>
</HTML>