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etandem.html
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<HTML>
<HEAD>
<TITLE>
EMBOSS: etandem
</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">
etandem
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Looks for tandem repeats in a nucleotide sequence
<H2>
Description
</H2>
<b>etandem</b> looks for tandem repeats in a sequence. It is normally
used after equicktandem has been run to identify potential repeat
sizes. It calculates a consensus for the repeat region and gives a
score for how many matches there are to the consensus - the number of
mismatches.
<p>
Input sequences are converted into ACGT or N (so ambiguity codes are ignored).
<br>
The score is +1 for a match, -1 for a mismatch.
<br>
The first copy of a repeat is ignored.
<br>
The highest score is kept for each start position and repeat size.
<p>
The lowest score to be reported is set by the threshold score. The
threshold score can be set on the command-line using the
<b>-threshold</b> qualifier, the default is 20. For perfect repeats, the
score is the length of the repeat (except for the first copy). Reduce
the threshold score a little if you wish to to allow mismatches. Each
mismatch scores -1 instead of +1 so it scores 2 less than a perfect
match of the same number of bases.
<p>
Running with a wide range of repeat sizes is inefficient. That is why
equicktandem was written - to give a rapid estimate of the major repeat
sizes.
<H2>
Usage
</H2>
<b>Here is a sample session with etandem</b>
<p>
The input sequence is the human herpesvirus tandem repeat.
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>etandem -noorigfile </b>
Looks for tandem repeats in a nucleotide sequence
Input nucleotide sequence: <b>tembl:L46634</b>
Minimum repeat size [10]: <b>6</b>
Maximum repeat size [6]: <b></b>
Output report [l46634.tan]: <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] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-minrepeat integer [10] Minimum repeat size (Integer, 2 or
higher)
-maxrepeat integer [Same as -minrepeat] Maximum repeat size
(Integer, same as -minrepeat or higher)
[-outfile] report [*.etandem] Output report file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-threshold integer [20] Threshold score (Any integer value)
-mismatch boolean Allow N as a mismatch
-uniform boolean Allow uniform consensus
-origfile outfile [*.etandem] Sanger Centre program tandem
output file (optional)
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
-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
"-origfile" associated qualifiers
-odirectory 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 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>
</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>Nucleotide sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-minrepeat</td>
<td>Minimum repeat size</td>
<td>Integer, 2 or higher</td>
<td>10</td>
</tr>
<tr>
<td>-maxrepeat</td>
<td>Maximum repeat size</td>
<td>Integer, same as -minrepeat or higher</td>
<td>Same as -minrepeat</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.etandem</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 colspan=4>(none)</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>-threshold</td>
<td>Threshold score</td>
<td>Any integer value</td>
<td>20</td>
</tr>
<tr>
<td>-mismatch</td>
<td>Allow N as a mismatch</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-uniform</td>
<td>Allow uniform consensus</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-origfile</td>
<td>Sanger Centre program tandem output file (optional)</td>
<td>Output file</td>
<td><i><*></i>.etandem</td>
</tr>
</table>
<H2>
Input file format
</H2>
The input for etandem is a nucleotide sequence USA.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:L46634' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:L46634</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID L46634; SV 1; linear; genomic DNA; STD; VRL; 1272 BP.
XX
AC L46634; L46689;
XX
DT 06-NOV-1995 (Rel. 45, Created)
DT 04-MAR-2000 (Rel. 63, Last updated, Version 3)
XX
DE Human herpesvirus 7 (clone ED132'1.2) telomeric repeat region.
XX
KW telomeric repeat.
XX
OS Human herpesvirus 7
OC Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae;
OC Roseolovirus.
XX
RN [1]
RP 1-1272
RX PUBMED; 7494318.
RA Secchiero P., Nicholas J., Deng H., Xiaopeng T., van Loon N., Ruvolo V.R.,
RA Berneman Z.N., Reitz M.S. Jr., Dewhurst S.;
RT "Identification of human telomeric repeat motifs at the genome termini of
RT human herpesvirus 7: structural analysis and heterogeneity";
RL J. Virol. 69(12):8041-8045(1995).
XX
FH Key Location/Qualifiers
FH
FT source 1..1272
FT /organism="Human herpesvirus 7"
FT /strain="JI"
FT /mol_type="genomic DNA"
FT /clone="ED132'1.2"
FT /db_xref="taxon:10372"
FT repeat_region 207..928
FT /note="long and complex repeat region composed of various
FT direct repeats, including TAACCC (TRS), degenerate copies
FT of TRS motifs and a 14-bp repeat, TAGGGCTGCGGCCC"
FT misc_signal 938..998
FT /note="pac2 motif"
FT misc_feature 1009
FT /note="right genome terminus (...ACA)"
XX
SQ Sequence 1272 BP; 346 A; 455 C; 222 G; 249 T; 0 other;
aagcttaaac tgaggtcaca cacgacttta attacggcaa cgcaacagct gtaagctgca 60
ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc 120
tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa 180
ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca 240
actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc 300
taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc 360
taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc 420
tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac 480
cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc 540
taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg 600
gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc 660
ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg 720
cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac 780
cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta 840
accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta 900
accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc 960
cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac 1020
gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt 1080
agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga 1140
aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca 1200
agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa 1260
gttttcaagc tt 1272
//
</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>etandem</b> writes a 'table' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: l46634.tan</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: etandem
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: etandem
# -noorigfile
# -sequence tembl:L46634
# -minrepeat 6
# Report_format: table
# Report_file: l46634.tan
########################################
#=======================================
#
# Sequence: L46634 from: 1 to: 1272
# HitCount: 5
#
# Threshold: 20
# Minrepeat: 6
# Maxrepeat: 6
# Mismatch: No
# Uniform: No
#
#=======================================
Start End Score Size Count Identity Consensus
793 936 120 6 24 93.8 acccta
283 420 90 6 23 84.8 taaccc
432 485 38 6 9 90.7 ccctaa
494 529 26 6 6 94.4 ccctaa
568 597 24 6 5 100.0 aaccct
#---------------------------------------
#---------------------------------------
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
Running with a wide range of repeat sizes is inefficient. That is why
equicktandem was written - to give a rapid estimate of the major repeat
sizes.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostics
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<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="einverted.html">einverted</a></td>
<td>Finds DNA inverted repeats</td>
</tr>
<tr>
<td><a href="equicktandem.html">equicktandem</a></td>
<td>Finds tandem repeats</td>
</tr>
<tr>
<td><a href="palindrome.html">palindrome</a></td>
<td>Looks for inverted repeats in a nucleotide sequence</td>
</tr>
</table>
<p>
Running with a wide range of repeat sizes is inefficient. That is why
equicktandem was written - to give a rapid estimate of the major repeat
sizes.
<H2>
Authors
</H2>
This program was originally written by
Richard Durbin (rd © sanger.ac.uk)
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.
<p>
This application was modified for inclusion in EMBOSS 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 25 May 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
</BODY>
</HTML>