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btwisted |
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btwisted reads a pure DNA sequence and calculates by simple arithmetic the probable overall twist of the sequence and the stacking energy.
% btwisted -auto tembl:ab000095 -sbegin 100 -send 120 |
Go to the input files for this example
Go to the output files for this example
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
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| 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 |
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.
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
//
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# 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 |
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:
| 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) |
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.