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   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

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; 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"


  [Part of this file has been deleted for brevity]

FT                   QPDRGEDAIAACFLINCLYEQNFVCKFAPREGFINYLTREVYRSYRQLRTQGFGGSGI
P
FT                   KAWAGIDLKVQPQEPLVLKDVENTDWRLLRGDTDVRVERKDPNQVELWGLKEGTYLFQ
L
FT                   TVTSSDHPEDTANVTVTVLSTKQTEDYCLASNKVGRCRGSFPRWYYDPTEQICKSFVY
G
FT                   GCLGNKNNYLREEECILACRGVQGPSMERRHPVCSGTCQPTQFRCSNGCCIDSFLECD
D
FT                   TPNCPDASDEAACEKYTSGFDELQRIHFPSDKGHCVDLPDTGLCKESIPRWYYNPFSE
H
FT                   CARFTYGGCYGNKNNFEEEQQCLESCRGISKKDVFGLRREIPIPSTGSVEMAVAVFLV
I
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        6
0
     ctgggaccgg aacctcggcg gacccggccc cacccaactc acctgcgcag gtcaccagca       12
0
     ccctcggaac ccagaggccc gcgctctgaa ggtgaccccc ctggggagga aggcgatggc       18
0
     ccctgcgagg acgatggccc gcgcccgcct cgccccggcc ggcatccctg ccgtcgcctt       24
0
     gtggcttctg tgcacgctcg gcctccaggg cacccaggcc gggccaccgc ccgcgccccc       30
0
     tgggctgccc gcgggagccg actgcctgaa cagctttacc gccggggtgc ctggcttcgt       36
0
     gctggacacc aacgcctcgg tcagcaacgg agctaccttc ctggagtccc ccaccgtgcg       42
0
     ccggggctgg gactgcgtgc gcgcctgctg caccacccag aactgcaact tggcgctagt       48
0
     ggagctgcag cccgaccgcg gggaggacgc catcgccgcc tgcttcctca tcaactgcct       54
0
     ctacgagcag aacttcgtgt gcaagttcgc gcccagggag ggcttcatca actacctcac       60
0
     gagggaagtg taccgctcct accgccagct gcggacccag ggctttggag ggtctgggat       66
0
     ccccaaggcc tgggcaggca tagacttgaa ggtacaaccc caggaacccc tggtgctgaa       72
0
     ggatgtggaa aacacagatt ggcgcctact gcggggtgac acggatgtca gggtagagag       78
0
     gaaagaccca aaccaggtgg aactgtgggg actcaaggaa ggcacctacc tgttccagct       84
0
     gacagtgact agctcagacc acccagagga cacggccaac gtcacagtca ctgtgctgtc       90
0
     caccaagcag acagaagact actgcctcgc atccaacaag gtgggtcgct gccggggctc       96
0
     tttcccacgc tggtactatg accccacgga gcagatctgc aagagtttcg tttatggagg      102
0
     ctgcttgggc aacaagaaca actaccttcg ggaagaagag tgcattctag cctgtcgggg      108
0
     tgtgcaaggc ccctccatgg aaaggcgcca tccagtgtgc tctggcacct gtcagcccac      114
0
     ccagttccgc tgcagcaatg gctgctgcat cgacagtttc ctggagtgtg acgacacccc      120
0
     caactgcccc gacgcctccg acgaggctgc ctgtgaaaaa tacacgagtg gctttgacga      126
0
     gctccagcgc atccatttcc ccagtgacaa agggcactgc gtggacctgc cagacacagg      132
0
     actctgcaag gagagcatcc cgcgctggta ctacaacccc ttcagcgaac actgcgcccg      138
0
     ctttacctat ggtggttgtt atggcaacaa gaacaacttt gaggaagagc agcagtgcct      144
0
     cgagtcttgt cgcggcatct ccaagaagga tgtgtttggc ctgaggcggg aaatccccat      150
0
     tcccagcaca ggctctgtgg agatggctgt cgcagtgttc ctggtcatct gcattgtggt      156
0
     ggtggtagcc atcttgggtt actgcttctt caagaaccag agaaaggact tccacggaca      162
0
     ccaccaccac ccaccaccca cccctgccag ctccactgtc tccactaccg aggacacgga      168
0
     gcacctggtc tataaccaca ccacccggcc cctctgagcc tgggtctcac cggctctcac      174
0
     ctggccctgc ttcctgcttg ccaaggcaga ggcctgggct gggaaaaact ttggaaccag      180
0
     actcttgcct gtttcccagg cccactgtgc ctcagagacc agggctccag cccctcttgg      186
0
     agaagtctca gctaagctca cgtcctgaga aagctcaaag gtttggaagg agcagaaaac      192
0
     ccttgggcca gaagtaccag actagatgga cctgcctgca taggagtttg gaggaagttg      198
0
     gagttttgtt tcctctgttc aaagctgcct gtccctaccc catggtgcta ggaagaggag      204
0
     tggggtggtg tcagaccctg gaggccccaa ccctgtcctc ccgagctcct cttccatgct      210
0
     gtgcgcccag ggctgggagg aaggacttcc ctgtgtagtt tgtgctgtaa agagttgctt      216
0
     tttgtttatt taatgctgtg gcatgggtga agaggagggg aagaggcctg tttggcctct      222
0
     ctgtcctctc ttcctcttcc cccaagattg agctctctgc ccttgatcag ccccaccctg      228
0
     gcctagacca gcagacagag ccaggagagg ctcagctgca ttccgcagcc cccaccccca      234
0
     aggttctcca acatcacagc ccagcccacc cactgggtaa taaaagtggt ttgtggaaa       239
9
//

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:
     * . (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       Bending and curvature plot in B-DNA
   chaos        Create a chaos game representation plot for a sequence
   compseq      Count composition of dimer/trimer/etc words in a sequence
   dan          Calculates DNA RNA/DNA melting temperature
   freak        Residue/base frequency table or plot
   isochore     Plots isochores in large DNA sequences
   sirna        Finds siRNA duplexes in mRNA
   wordcount    Counts 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