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EMBOSS: btwisted
btwisted

 

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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:6.4.0.0

   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
   -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 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
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-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 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   Ensembl-Gn; ENSG00000166145; Homo_sapiens.
DR   Ensembl-Tr; ENST00000344051; Homo_sapiens.
DR   Ensembl-Tr; ENST00000431806; Homo_sapiens.
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"


  [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 Calculates nucleic acid melting temperature
density Draw a nucleic acid density plot
einverted Finds inverted repeats in nucleotide sequences
freak Generate residue/base frequency table or plot
isochore Plots isochores in DNA sequences
sirna Finds 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