EMBOSS: btwisted

| btwisted

## Wiki

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## 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:6.5.6.0

       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
       -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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.btwisted
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-angledata | datafile | DNA base pair twist angle data file | Data file | Eangles.dat
-energydata | datafile | DNA base pair stacking energies data file | Data file | Eenergy.dat
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1 -sbegin_sequence | integer | Start of the sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of the sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 © 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 © 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