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<HTML>
<HEAD>
<TITLE>
EMBOSS: helixturnhelix
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
helixturnhelix
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Report nucleic acid binding motifs
<H2>
Description
</H2>
<b>helixturnhelix</b> uses the method of Dodd and Egan and finds
helix-turn-helix nucleic acid binding motifs in proteins.
<p>
The helix-turn-helix motif was originally identified as the DNA-binding
domain of phage repressors. One alpha-helix lies in the wide groove of
DNA; the other lies at an angle across DNA.
<p>
<H2>
Usage
</H2>
<b>Here is a sample session with helixturnhelix</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>helixturnhelix </b>
Report nucleic acid binding motifs
Input protein sequence(s): <b>tsw:laci_ecoli</b>
Output report [laci_ecoli.hth]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
[-outfile] report [*.helixturnhelix] Output report file name
Additional (Optional) qualifiers:
-mean float [238.71] Mean value (Number from 1.000 to
10000.000)
-sd float [293.61] Standard Deviation value (Number
from 1.000 to 10000.000)
-minsd float [2.5] Minimum SD (Number from 0.000 to
100.000)
-eightyseven boolean Use the old (1987) weight data
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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
-rformat2 string Report format
-rname2 string Base file name
-rextension2 string File name extension
-rdirectory2 string Output directory
-raccshow2 boolean Show accession number in the report
-rdesshow2 boolean Show description in the report
-rscoreshow2 boolean Show the score in the report
-rusashow2 boolean Show the full USA in the report
-rmaxall2 integer Maximum total hits to report
-rmaxseq2 integer Maximum hits to report for one sequence
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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.helixturnhelix</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-mean</td>
<td>Mean value</td>
<td>Number from 1.000 to 10000.000</td>
<td>238.71</td>
</tr>
<tr>
<td>-sd</td>
<td>Standard Deviation value</td>
<td>Number from 1.000 to 10000.000</td>
<td>293.61</td>
</tr>
<tr>
<td>-minsd</td>
<td>Minimum SD</td>
<td>Number from 0.000 to 100.000</td>
<td>2.5</td>
</tr>
<tr>
<td>-eightyseven</td>
<td>Use the old (1987) weight data</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>helixturnhelix</b> reads one or more protein sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tsw:laci_ecoli' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:laci_ecoli</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID LACI_ECOLI Reviewed; 360 AA.
AC P03023; O09196; P71309; Q2MC79; Q47338;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2003, sequence version 3.
DT 20-MAR-2007, entry version 87.
DE Lactose operon repressor.
GN Name=lacI; OrderedLocusNames=b0345, JW0336;
OS Escherichia coli.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0;
RA Farabaugh P.J.;
RT "Sequence of the lacI gene.";
RL Nature 274:765-769(1978).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Chen J., Matthews K.K.S.M.;
RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Marsh S.;
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA Mau B., Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1474(1997).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains
<font color=red> [Part of this file has been deleted for brevity]</font>
DR Pfam; PF00532; Peripla_BP_1; 1.
DR PRINTS; PR00036; HTHLACI.
DR SMART; SM00354; HTH_LACI; 1.
DR PROSITE; PS00356; HTH_LACI_1; 1.
DR PROSITE; PS50932; HTH_LACI_2; 1.
KW 3D-structure; Complete proteome; Direct protein sequencing;
KW DNA-binding; Repressor; Transcription; Transcription regulation.
FT CHAIN 1 360 Lactose operon repressor.
FT /FTId=PRO_0000107963.
FT DOMAIN 1 58 HTH lacI-type.
FT DNA_BIND 6 25 H-T-H motif.
FT VARIANT 282 282 Y -> D (in T41 mutant).
FT MUTAGEN 17 17 Y->H: Broadening of specificity.
FT MUTAGEN 22 22 R->N: Recognizes an operator variant.
FT CONFLICT 286 286 L -> S (in Ref. 1, 4 and 7).
FT STRAND 63 69
FT HELIX 74 89
FT STRAND 93 98
FT STRAND 101 103
FT HELIX 104 115
FT TURN 116 118
FT STRAND 122 126
FT HELIX 130 139
FT TURN 140 142
FT STRAND 145 150
FT STRAND 154 156
FT STRAND 158 161
FT HELIX 163 177
FT STRAND 181 186
FT HELIX 192 207
FT STRAND 213 217
FT HELIX 222 234
FT STRAND 240 246
FT HELIX 247 259
FT TURN 265 267
FT STRAND 268 271
FT HELIX 277 281
FT STRAND 282 284
FT STRAND 287 290
FT HELIX 293 308
FT STRAND 314 319
FT STRAND 322 324
FT HELIX 354 356
SQ SEQUENCE 360 AA; 38590 MW; 347A8DEE92D736CB CRC64;
MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ
SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS
GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ
QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT
AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPLTTIK QDFRLLGQTS
VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, where 'xxx' is replaced by
the name of the required format. The available format names are: embl,
genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
feattable, motif, regions, seqtable, simple, srs, table, tagseq
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
<p>
By default <b>helixturnhelix</b> writes a 'motif' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: laci_ecoli.hth</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: helixturnhelix
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: helixturnhelix
# -sequence tsw:laci_ecoli
# Report_format: motif
# Report_file: laci_ecoli.hth
########################################
#=======================================
#
# Sequence: LACI_ECOLI from: 1 to: 360
# HitCount: 1
#
# Hits above +2.50 SD (972.73)
#
#=======================================
Maximum_score_at at "*"
(1) Score 2160.000 length 22 at residues 4->25
*
Sequence: VTLYDVAEYAGVSYQTVSRVVN
| |
4 25
Standard_deviations: 6.54
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 1
#---------------------------------------
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
<p>
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.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
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".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<p>
The data files are stored in the standard EMBOSS data directory. The
names are:
<p>
<ul>
<li> Ehth.dat matrix file
<li> Ehth87.dat 1987 shorter matrix file
</ul>
<p>
The old (1987) data has a motif length of 20 residues, whilst the default
data (Ehth.dat) has a motif length of 22 residues.
<p>
With care these can be replaced to suit your data sets. If the files are
placed in the following directories they will be used in preference to
the files in the EMBOSS distribution data directory:
<ul>
<li> . (your current directory)
<li> .embossdata
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
Here is the default file:
<pre>
# Amino acid counts for 91 Helix-turn-helix (presumed) protein motifs
# from Dodd IB and Egan JB (1990) Nucl. Acids. Res. 18:5019-5026.
#
Sample: 91 aligned sequences
#
# R 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Total Exp
# - -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- ----- ---
A 2 1 3 14 10 12 75 6 15 9 1 1 4 3 8 15 4 4 4 11 0 10 212 995
C 0 0 1 1 0 0 0 0 0 3 3 1 1 0 0 0 0 0 0 1 0 3 14 106
D 0 1 0 1 14 0 0 14 1 0 5 0 1 2 0 0 0 0 1 1 0 2 43 556
E 4 5 0 11 26 0 0 16 9 3 3 0 3 12 13 0 0 2 0 1 13 6 127 669
F 4 0 4 0 0 4 0 1 0 10 0 0 0 0 1 0 0 1 1 1 22 0 49 358
G 9 7 1 4 0 0 8 0 0 0 50 0 6 0 7 1 0 3 1 1 0 4 102 761
H 4 3 1 1 2 0 0 3 2 0 5 0 3 3 0 2 0 2 4 5 0 2 42 225
I 10 0 13 3 2 15 0 4 9 4 0 17 0 2 0 1 31 1 4 8 16 1 141 583
K 4 4 6 11 12 1 1 14 11 0 5 2 2 7 2 1 0 5 8 4 5 15 120 516
L 16 1 17 0 1 35 0 3 12 31 0 22 0 2 1 1 22 1 1 12 20 0 198 954
M 7 0 2 1 1 1 0 0 5 7 1 10 0 0 2 0 2 0 0 2 0 1 42 275
N 0 8 0 1 0 0 0 2 1 1 14 0 8 1 4 2 0 4 9 0 0 11 66 383
P 1 6 0 1 0 0 0 0 0 0 0 0 3 13 7 0 0 0 0 0 0 3 34 403
Q 2 1 21 9 11 0 0 9 8 0 0 2 1 17 7 12 0 3 12 5 3 9 132 437
R 9 10 14 9 5 0 1 16 10 0 1 0 1 17 8 7 0 17 28 3 0 16 172 609
S 2 17 0 8 4 1 6 1 2 2 3 0 37 1 25 5 0 29 3 0 1 5 152 552
T 6 24 3 12 1 5 0 2 2 4 0 5 20 4 3 39 0 4 1 0 4 3 142 512
V 7 3 1 1 2 16 0 0 2 12 0 29 0 5 3 3 32 0 7 8 7 0 138 724
W 2 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 2 21 0 0 27 105
Y 2 0 4 3 0 1 0 0 2 4 0 1 1 2 0 2 0 15 5 7 0 0 49 267
</pre>
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>
Dodd I.B., Egan J.B. (1987)
"Systematic method for the detection of potential lambda cro-like
DNA-binding regions in proteins."
J. Mol. Biol. 194: 557-564.
<li>
Dodd I.B., Egan J.B. (1990)
"Improved detection of helix-turn-helix DNA-binding motifs in
protein sequences."
Nucleic Acids Res. 18: 5019-5026.
</ol>
<H2>
Warnings
</H2>
The program will warn you if the data file is not mathematically
accurate.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It exits with status 0 unless an error is reported.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="antigenic.html">antigenic</a></td>
<td>Finds antigenic sites in proteins</td>
</tr>
<tr>
<td><a href="digest.html">digest</a></td>
<td>Protein proteolytic enzyme or reagent cleavage digest</td>
</tr>
<tr>
<td><a href="epestfind.html">epestfind</a></td>
<td>Finds PEST motifs as potential proteolytic cleavage sites</td>
</tr>
<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>Protein pattern search</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>
<tr>
<td><a href="garnier.html">garnier</a></td>
<td>Predicts protein secondary structure</td>
</tr>
<tr>
<td><a href="hmoment.html">hmoment</a></td>
<td>Hydrophobic moment calculation</td>
</tr>
<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>Find protein sequence regions with a biased composition</td>
</tr>
<tr>
<td><a href="patmatdb.html">patmatdb</a></td>
<td>Search a protein sequence with a motif</td>
</tr>
<tr>
<td><a href="patmatmotifs.html">patmatmotifs</a></td>
<td>Search a PROSITE motif database with a protein sequence</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>
<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>Displays proteins as a helical net</td>
</tr>
<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>Shows protein sequences as helices</td>
</tr>
<tr>
<td><a href="preg.html">preg</a></td>
<td>Regular expression search of a protein sequence</td>
</tr>
<tr>
<td><a href="pscan.html">pscan</a></td>
<td>Scans proteins using PRINTS</td>
</tr>
<tr>
<td><a href="sigcleave.html">sigcleave</a></td>
<td>Reports protein signal cleavage sites</td>
</tr>
<tr>
<td><a href="tmap.html">tmap</a></td>
<td>Displays membrane spanning regions</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
Original program "HELIXTURNHELIX" (EGCG 1990) by
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Completed 11th March 1999
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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</HTML>