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<HTML>
<HEAD>
<TITLE>
EMBOSS: btwisted
</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="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
btwisted
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Calculates the twisting in a B-DNA sequence
<H2>
Description
</H2>
<b>btwisted</b> takes a region of a pure DNA sequence and calculates
by simple arithmetic the probable overall twist of the sequence and
the stacking energy.
<H2>
Usage
</H2>
<b>Here is a sample session with btwisted</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>btwisted -auto tembl:ab000095 -sbegin 100 -send 120 </b>
</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>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-outfile] outfile [*.btwisted] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-angledata datafile [Eangles.dat] DNA base pair twist angle data
file
-energydata datafile [Eenergy.dat] DNA base pair stacking
energies data file
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
"-outfile" associated qualifiers
-odirectory2 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Nucleotide sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.btwisted</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-angledata</td>
<td>DNA base pair twist angle data file</td>
<td>Data file</td>
<td>Eangles.dat</td>
</tr>
<tr>
<td>-energydata</td>
<td>DNA base pair stacking energies data file</td>
<td>Data file</td>
<td>Eenergy.dat</td>
</tr>
</table>
<H2>
Input file format
</H2>
Nucleic acid sequence USA.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:ab000095' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:ab000095</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID AB000095; SV 1; linear; mRNA; STD; HUM; 2399 BP.
XX
AC AB000095;
XX
DT 10-MAR-1998 (Rel. 54, Created)
DT 14-APR-2005 (Rel. 83, Last updated, Version 2)
XX
DE Homo sapiens mRNA for hepatocyte growth factor activator inhibitor,
DE complete cds.
XX
KW hepatocyte growth factor activator inhibitor.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-2399
RA Denda K.;
RT ;
RL Submitted (24-DEC-1996) to the EMBL/GenBank/DDBJ databases.
RL Kimitoshi Denda, Tokyo Institute of Technology, Department of Life Science;
RL 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 227, Japan
RL (E-mail:kdenda@bio.titech.ac.jp, Tel:45-924-5702, Fax:45-924-5771)
XX
RN [2]
RX DOI; 10.1074/jbc.272.10.6370.
RX PUBMED; 9045658.
RA Shimomura T., Denda K., Kitamura A., Kawaguchi T., Kito M., Kondo J.,
RA Kagaya S., Qin L., Takata H., Miyazawa K., Kitamura N.;
RT "Hepatocyte growth factor activator inhibitor, a novel Kunitz-type serine
RT protease inhibitor";
RL J. Biol. Chem. 272(10):6370-6376(1997).
XX
DR H-InvDB; HIT000057890.
XX
FH Key Location/Qualifiers
FH
FT source 1..2399
FT /organism="Homo sapiens"
FT /mol_type="mRNA"
FT /db_xref="taxon:9606"
FT CDS 176..1717
FT /product="hepatocyte growth factor activator inhibitor"
FT /db_xref="GDB:118879"
FT /db_xref="GOA:O43278"
FT /db_xref="HGNC:11246"
FT /db_xref="PDB:1YC0"
FT /db_xref="UniProtKB/Swiss-Prot:O43278"
<font color=red> [Part of this file has been deleted for brevity]</font>
FT QPDRGEDAIAACFLINCLYEQNFVCKFAPREGFINYLTREVYRSYRQLRTQGFGGSGIP
FT KAWAGIDLKVQPQEPLVLKDVENTDWRLLRGDTDVRVERKDPNQVELWGLKEGTYLFQL
FT TVTSSDHPEDTANVTVTVLSTKQTEDYCLASNKVGRCRGSFPRWYYDPTEQICKSFVYG
FT GCLGNKNNYLREEECILACRGVQGPSMERRHPVCSGTCQPTQFRCSNGCCIDSFLECDD
FT TPNCPDASDEAACEKYTSGFDELQRIHFPSDKGHCVDLPDTGLCKESIPRWYYNPFSEH
FT CARFTYGGCYGNKNNFEEEQQCLESCRGISKKDVFGLRREIPIPSTGSVEMAVAVFLVI
FT CIVVVVAILGYCFFKNQRKDFHGHHHHPPPTPASSTVSTTEDTEHLVYNHTTRPL"
FT polyA_signal 2379..2384
XX
SQ Sequence 2399 BP; 490 A; 777 C; 684 G; 448 T; 0 other;
cggccgagcc cagctctccg agcaccgggt cggaagccgc gacccgagcc gcgcaggaag 60
ctgggaccgg aacctcggcg gacccggccc cacccaactc acctgcgcag gtcaccagca 120
ccctcggaac ccagaggccc gcgctctgaa ggtgaccccc ctggggagga aggcgatggc 180
ccctgcgagg acgatggccc gcgcccgcct cgccccggcc ggcatccctg ccgtcgcctt 240
gtggcttctg tgcacgctcg gcctccaggg cacccaggcc gggccaccgc ccgcgccccc 300
tgggctgccc gcgggagccg actgcctgaa cagctttacc gccggggtgc ctggcttcgt 360
gctggacacc aacgcctcgg tcagcaacgg agctaccttc ctggagtccc ccaccgtgcg 420
ccggggctgg gactgcgtgc gcgcctgctg caccacccag aactgcaact tggcgctagt 480
ggagctgcag cccgaccgcg gggaggacgc catcgccgcc tgcttcctca tcaactgcct 540
ctacgagcag aacttcgtgt gcaagttcgc gcccagggag ggcttcatca actacctcac 600
gagggaagtg taccgctcct accgccagct gcggacccag ggctttggag ggtctgggat 660
ccccaaggcc tgggcaggca tagacttgaa ggtacaaccc caggaacccc tggtgctgaa 720
ggatgtggaa aacacagatt ggcgcctact gcggggtgac acggatgtca gggtagagag 780
gaaagaccca aaccaggtgg aactgtgggg actcaaggaa ggcacctacc tgttccagct 840
gacagtgact agctcagacc acccagagga cacggccaac gtcacagtca ctgtgctgtc 900
caccaagcag acagaagact actgcctcgc atccaacaag gtgggtcgct gccggggctc 960
tttcccacgc tggtactatg accccacgga gcagatctgc aagagtttcg tttatggagg 1020
ctgcttgggc aacaagaaca actaccttcg ggaagaagag tgcattctag cctgtcgggg 1080
tgtgcaaggc ccctccatgg aaaggcgcca tccagtgtgc tctggcacct gtcagcccac 1140
ccagttccgc tgcagcaatg gctgctgcat cgacagtttc ctggagtgtg acgacacccc 1200
caactgcccc gacgcctccg acgaggctgc ctgtgaaaaa tacacgagtg gctttgacga 1260
gctccagcgc atccatttcc ccagtgacaa agggcactgc gtggacctgc cagacacagg 1320
actctgcaag gagagcatcc cgcgctggta ctacaacccc ttcagcgaac actgcgcccg 1380
ctttacctat ggtggttgtt atggcaacaa gaacaacttt gaggaagagc agcagtgcct 1440
cgagtcttgt cgcggcatct ccaagaagga tgtgtttggc ctgaggcggg aaatccccat 1500
tcccagcaca ggctctgtgg agatggctgt cgcagtgttc ctggtcatct gcattgtggt 1560
ggtggtagcc atcttgggtt actgcttctt caagaaccag agaaaggact tccacggaca 1620
ccaccaccac ccaccaccca cccctgccag ctccactgtc tccactaccg aggacacgga 1680
gcacctggtc tataaccaca ccacccggcc cctctgagcc tgggtctcac cggctctcac 1740
ctggccctgc ttcctgcttg ccaaggcaga ggcctgggct gggaaaaact ttggaaccag 1800
actcttgcct gtttcccagg cccactgtgc ctcagagacc agggctccag cccctcttgg 1860
agaagtctca gctaagctca cgtcctgaga aagctcaaag gtttggaagg agcagaaaac 1920
ccttgggcca gaagtaccag actagatgga cctgcctgca taggagtttg gaggaagttg 1980
gagttttgtt tcctctgttc aaagctgcct gtccctaccc catggtgcta ggaagaggag 2040
tggggtggtg tcagaccctg gaggccccaa ccctgtcctc ccgagctcct cttccatgct 2100
gtgcgcccag ggctgggagg aaggacttcc ctgtgtagtt tgtgctgtaa agagttgctt 2160
tttgtttatt taatgctgtg gcatgggtga agaggagggg aagaggcctg tttggcctct 2220
ctgtcctctc ttcctcttcc cccaagattg agctctctgc ccttgatcag ccccaccctg 2280
gcctagacca gcagacagag ccaggagagg ctcagctgca ttccgcagcc cccaccccca 2340
aggttctcca acatcacagc ccagcccacc cactgggtaa taaaagtggt ttgtggaaa 2399
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: ab000095.btwisted</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Output from BTWISTED
# Twisting calculated from 100 to 120 of AB000095
Total twist (degrees): 681.1
Total turns : 1.89
Average bases per turn: 11.10
Total stacking energy : -179.34
Average stacking energy per dinucleotide: -8.97
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
The program reads in two data files.
<P>
The first is prompted for by:
<P>
"File containing base pair twist angles"
<P>
<br>
This is the data file 'Eangles.dat' by default.
<P>
This consists of the data:
<P>
<pre>
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
</pre>
<p>
The second is prompted for by:
<P>
"File containing base pair stacking energies"
<br>
This is the data file 'Eenergy.dat' by default.
<P>
This consists of the data:
<P>
<pre>
#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
</pre>
<P>
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.
<P>
<p>
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.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
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".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<p>
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
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.
<H2>
Diagnostic Error Messages
</H2>
"Incomplete table"
<BR>
You have supplied data files for either the angles or energies that do
not contain the fulll required set of possible dinucleotides.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
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.
<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="banana.html">banana</a></td>
<td>Bending and curvature plot in B-DNA</td>
</tr>
<tr>
<td><a href="chaos.html">chaos</a></td>
<td>Create a chaos game representation plot for a sequence</td>
</tr>
<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Count composition of dimer/trimer/etc words in a sequence</td>
</tr>
<tr>
<td><a href="dan.html">dan</a></td>
<td>Calculates DNA RNA/DNA melting temperature</td>
</tr>
<tr>
<td><a href="freak.html">freak</a></td>
<td>Residue/base frequency table or plot</td>
</tr>
<tr>
<td><a href="isochore.html">isochore</a></td>
<td>Plots isochores in large DNA sequences</td>
</tr>
<tr>
<td><a href="sirna.html">sirna</a></td>
<td>Finds siRNA duplexes in mRNA</td>
</tr>
<tr>
<td><a href="wordcount.html">wordcount</a></td>
<td>Counts words of a specified size in a DNA sequence</td>
</tr>
</table>
<H2>
Author(s)
</H2>
David Martin (dmartin © rfcgr.mrc.ac.uk)
<br>
and
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
This application was written during the first Scandinavian EMBOSS Workshop.
<H2>
History
</H2>
Written (Sept 2000) - David Martin & Alan Bleasby.
<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>
|
