| 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

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

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

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence USA | Readable sequence | Required
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.btwisted
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-angledata | File containing base pair twist angles | Any string is accepted | Eangles.dat
-energydata | File containing base pair stacking energies | Any string is accepted | 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:

- . (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 | Counts the 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)

This application was written by David Martin (dmartin © hgmp.mrc.ac.uk)
and Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
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