btwisted

 

Function

Calculates the twisting in a B-DNA sequence

Description

btwisted takes a region of 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

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -angledata          datafile   File containing base pair twist angles
   -energydata         datafile   File containing base pair stacking energies

   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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
[-outfile]
(Parameter 2)
Output file name Output file <sequence>.btwisted
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-angledata File containing base pair twist angles Data file Eangles.dat
-energydata File containing base pair stacking energies Data file Eenergy.dat

Input file format

Nucleic acid sequence USA.

Input files for usage example

'tembl:ab000095' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:ab000095

ID   AB000095   standard; RNA; HUM; 2399 BP.
XX
AC   AB000095;
XX
SV   AB000095.1
XX
DT   10-MAR-1998 (Rel. 54, Created)
DT   10-MAR-1998 (Rel. 54, Last updated, Version 1)
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; Primates; Catarrhini; Hominidae; 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]
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. 272:6370-6376(1997).
XX
DR   SWISS-PROT; O43278; SPT1_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2399
FT                   /db_xref="taxon:9606"
FT                   /sequenced_mol="cDNA to mRNA"
FT                   /organism="Homo sapiens"
FT   CDS             176..1717
FT                   /db_xref="SWISS-PROT:O43278"
FT                   /product="hepatocyte growth factor activator inhibitor"
FT                   /protein_id="BAA25014.1"
FT                   /translation="MAPARTMARARLAPAGIPAVALWLLCTLGLQGTQAGPPPAPPGLP
FT                   AGADCLNSFTAGVPGFVLDTNASVSNGATFLESPTVRRGWDCVRACCTTQNCNLALVEL
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 reads in two data files.

The first is prompted for by:

"File containing base pair twist angles"


This is the data file 'Eangles.dat' by default.

This 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

The second is prompted for by:

"File containing base pair stacking energies"
This is the data file 'Eenergy.dat' by default.

This 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

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.

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:

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 nameDescription
bananaBending and curvature plot in B-DNA
chaosCreate a chaos game representation plot for a sequence
compseqCount composition of dimer/trimer/etc words in a sequence
danCalculates DNA RNA/DNA melting temperature
freakResidue/base frequency table or plot
isochorePlots isochores in large DNA sequences
sirnaFinds siRNA duplexes in mRNA
wordcountCounts words of a specified size in a DNA sequence

Author(s)

David Martin (dmartin © rfcgr.mrc.ac.uk)
and Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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