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btwisted
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Calculate the twisting in a B-DNA sequence
Description
btwisted reads a pure DNA sequence and calculates by simple arithmetic
the probable overall twist of the sequence and the stacking energy.
Usage
Here is a sample session with btwisted
% btwisted -auto tembl:ab000095 -sbegin 100 -send 120
Go to the input files for this example
Go to the output files for this example
Command line arguments
Calculate the twisting in a B-DNA sequence
Version: EMBOSS:6.6.0.0
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
-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
"-outfile" associated qualifiers
-odirectory2 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
Input file format
btwisted reads a single nucleotide sequence.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier
-sformat xxx, where 'xxx' is replaced by the name of the required
format. The available format names are: gff (gff3), gff2, embl (em),
genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
information on sequence formats.
Input files for usage example
'tembl:ab000095' is a sequence entry in the example nucleic acid
database 'tembl'
Database entry: tembl:ab000095
ID AB000095; SV 1; linear; mRNA; STD; HUM; 2399 BP.
XX
AC AB000095;
XX
DT 10-MAR-1998 (Rel. 54, Created)
DT 07-OCT-2008 (Rel. 97, Last updated, Version 3)
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 INSDC.
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 Ensembl-Gn; ENSG00000166145; Homo_sapiens.
DR Ensembl-Tr; ENST00000344051; Homo_sapiens.
DR Ensembl-Tr; ENST00000431806; Homo_sapiens.
DR Ensembl-Tr; ENST00000536281; Homo_sapiens.
DR Ensembl-Tr; ENST00000562057; Homo_sapiens.
DR Ensembl-Tr; ENST00000563656; Homo_sapiens.
DR Ensembl-Tr; ENST00000564375; Homo_sapiens.
DR Ensembl-Tr; ENST00000566928; Homo_sapiens.
DR Ensembl-Tr; ENST00000568580; Homo_sapiens.
DR Ensembl-Tr; ENST00000568823; Homo_sapiens.
DR Ensembl-Tr; ENST00000569589; Homo_sapiens.
XX
FH Key Location/Qualifiers
FH
FT source 1..2399
[Part of this file has been deleted for brevity]
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
//
Output file format
Output files for usage example
File: ab000095.btwisted
# 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
Data files
The program requires two data files. A file (Eangles.dat by default)
containing base pair twist angles, and another (Eenergy.dat) containing
base pair stacking energies. No check is made that all dinucleotides
are listed in the files and so read for their 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.
Eangles.dat 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
'Eenergy.dat' 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
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:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
Notes
None.
References
None.
Warnings
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.
Diagnostic Error Messages
"Incomplete table"
You have supplied data files for either the angles or energies that do
not contain the fulll required set of possible dinucleotides.
Exit status
It always exits with status 0.
Known bugs
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.
See also
Program name Description
banana Plot bending and curvature data for B-DNA
chaos Draw a chaos game representation plot for a nucleotide sequence
compseq Calculate the composition of unique words in sequences
dan Calculate nucleic acid melting temperature
density Draw a nucleic acid density plot
einverted Find inverted repeats in nucleotide sequences
freak Generate residue/base frequency table or plot
isochore Plot isochores in DNA sequences
sirna Find siRNA duplexes in mRNA
wordcount Count and extract unique words in molecular sequence(s)
Author(s)
David Martin
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author. and
Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
This application was written during the first Scandinavian EMBOSS
Workshop.
History
Written (Sept 2000) - David Martin & Alan Bleasby.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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