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<HTML>
<HEAD>
<TITLE>
EMBOSS: einverted
</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">
einverted
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Finds DNA inverted repeats
<H2>
Description
</H2>
<b>einverted</b> looks for inverted repeats (stem loops) in a nucleotide
sequence.
<p>
It will find inverted repeats that include a proprtion of mismatches and
gaps (bulges in the stem loop).
<H2>Algorithm</H2>
It works by finding alignments between the sequence and its reverse
complement that exceed a threshold score. Gaps and Mismatches are
assigned a penalty (negative) score. Matches are assigned a positive
score. The score is calculated by summing the values of each match, the
penalties of each mismatch and the large penalties of any gaps. Any
region whose score exceeds the threshold is reported.
<p>
<b>einverted</b> uses dynamic programming and thus is guaranteed to find
the optimal alignment, but is slower than, for example, a self-by-self BLAST.
It can find multiple inverted repeats in a sequence.
<p>
<b>einverted</b> does not report overlapping matches.
<p>
The original "inverted" program was written to annotate the nematode
genome. Excluding overlapping repeats saved problems with simple repeat
sequences in this genome.
<H2>
Usage
</H2>
<b>Here is a sample session with einverted</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>einverted tembl:d00596 </b>
Finds DNA inverted repeats
Gap penalty [12]: <b></b>
Minimum score threshold [50]: <b></b>
Match score [3]: <b></b>
Mismatch score [-4]: <b></b>
Sanger Centre program inverted output file [d00596.inv]: <b></b>
File for sequence of regions of inverted repeats. [d00596.fasta]: <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 Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-gap integer [12] Gap penalty (Any integer value)
-threshold integer [50] Minimum score threshold (Any integer
value)
-match integer [3] Match score (Any integer value)
-mismatch integer [-4] Mismatch score (Any integer value)
[-outfile] outfile [*.einverted] Sanger Centre program inverted
output file
[-outseq] seqout [<sequence>.<format>] The sequence of the
inverted repeat regions without gap
characters.
Additional (Optional) qualifiers:
-maxrepeat integer [2000] Maximum separation between the start
of repeat and the end of the inverted repeat
(the default is 2000 bases). (Any integer
value)
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
-odirectory2 string Output directory
"-outseq" associated qualifiers
-osformat3 string Output seq format
-osextension3 string File name extension
-osname3 string Base file name
-osdirectory3 string Output directory
-osdbname3 string Database name to add
-ossingle3 boolean Separate file for each entry
-oufo3 string UFO features
-offormat3 string Features format
-ofname3 string Features file name
-ofdirectory3 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>
</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(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-gap</td>
<td>Gap penalty</td>
<td>Any integer value</td>
<td>12</td>
</tr>
<tr>
<td>-threshold</td>
<td>Minimum score threshold</td>
<td>Any integer value</td>
<td>50</td>
</tr>
<tr>
<td>-match</td>
<td>Match score</td>
<td>Any integer value</td>
<td>3</td>
</tr>
<tr>
<td>-mismatch</td>
<td>Mismatch score</td>
<td>Any integer value</td>
<td>-4</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Sanger Centre program inverted output file</td>
<td>Output file</td>
<td><i><*></i>.einverted</td>
</tr>
<tr>
<td>[-outseq]<br>(Parameter 3)</td>
<td>The sequence of the inverted repeat regions without gap characters.</td>
<td>Writeable sequence</td>
<td><i><*></i>.<i>format</i></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>-maxrepeat</td>
<td>Maximum separation between the start of repeat and the end of the inverted repeat (the default is 2000 bases).</td>
<td>Any integer value</td>
<td>2000</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>
The input for <b>einverted</b> is a nucleotide sequence
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:d00596' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:d00596</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID D00596; SV 1; linear; genomic DNA; STD; HUM; 18596 BP.
XX
AC D00596;
XX
DT 17-JUL-1991 (Rel. 28, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 3)
XX
DE Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7,
DE complete cds.
XX
KW thymidylate syntase.
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 1-18596
RX PUBMED; 2243092.
RA Kaneda S., Nalbantoglu J., Takeishi K., Shimizu K., Gotoh O., Seno T.,
RA Ayusawa D.;
RT "Structural and functional analysis of the human thymidylate synthase
RT gene.";
RL J. Biol. Chem. 265(33):20277-20284(1990).
XX
DR GDB; 163670.
DR GDB; 182340.
XX
CC These data kindly submitted in computer readable form by:
CC Sumiko Kaneda
CC National Institute of Genetics
CC 1111 Yata
CC Mishima 411
CC Japan
CC Phone: +81-559-72-2732
CC Fax: +81-559-71-3651
XX
FH Key Location/Qualifiers
FH
FT source 1..18596
FT /organism="Homo sapiens"
FT /chromosome="18"
FT /map="18p11.32"
FT /mol_type="genomic DNA"
FT /clone="lambdaHTS-1 and lambdaHTS-3"
FT /db_xref="taxon:9606"
FT repeat_unit 1..148
FT /note="Alu sequence"
FT repeat_unit 202..477
<font color=red> [Part of this file has been deleted for brevity]</font>
ttttgttttt agcttcagcg agaacccaga cctttcccaa agctcaggat tcttcgaaaa 15660
gttgagaaaa ttgatgactt caaagctgaa gactttcaga ttgaagggta caatccgcat 15720
ccaactatta aaatggaaat ggctgtttag ggtgctttca aaggagctcg aaggatattg 15780
tcagtcttta ggggttgggc tggatgccga ggtaaaagtt ctttttgctc taaaagaaaa 15840
aggaactagg tcaaaaatct gtccgtgacc tatcagttat taatttttaa ggatgttgcc 15900
actggcaaat gtaactgtgc cagttctttc cataataaaa ggctttgagt taactcactg 15960
agggtatctg acaatgctga ggttatgaac aaagtgagga gaatgaaatg tatgtgctct 16020
tagcaaaaac atgtatgtgc atttcaatcc cacgtactta taaagaaggt tggtgaattt 16080
cacaagctat ttttggaata tttttagaat attttaagaa tttcacaagc tattccctca 16140
aatctgaggg agctgagtaa caccatcgat catgatgtag agtgtggtta tgaactttaa 16200
agttatagtt gttttatatg ttgctataat aaagaagtgt tctgcattcg tccacgcttt 16260
gttcattctg tactgccact tatctgctca gttccttcct aaaatagatt aaagaactct 16320
ccttaagtaa acatgtgctg tattctggtt tggatgctac ttaaaagagt atattttaga 16380
aataatagtg aatatatttt gccctatttt tctcatttta actgcatctt atcctcaaaa 16440
tataatgacc atttaggata gagttttttt tttttttttt taaactttta taaccttaaa 16500
gggttatttt aaaataatct atggactacc attttgccct cattagcttc agcatggtgt 16560
gacttctcta ataatatgct tagattaagc aaggaaaaga tgcaaaacca cttcggggtt 16620
aatcagtgaa atatttttcc cttcgttgca taccagatac ccccggtgtt gcacgactat 16680
ttttattctg ctaatttatg acaagtgtta aacagaacaa ggaattattc caacaagtta 16740
tgcaacatgt tgcttatttt caaattacag tttaatgtct aggtgccagc ccttgatata 16800
gctatttttg taagaacatc ctcctggact ttgggttagt taaatctaaa cttatttaag 16860
gattaagtag gataacgtgc attgatttgc taaaagaatc aagtaataat tacttagctg 16920
attcctgagg gtggtatgac ttctagctga actcatcttg atcggtagga ttttttaaat 16980
ccatttttgt aaaactattt ccaagaaatt ttaagccctt tcacttcaga aagaaaaaag 17040
ttgttggggc tgagcactta attttcttga gcaggaagga gtttcttcca aacttcacca 17100
tctggagact ggtgtttctt tacagattcc tccttcattt ctgttgagta gccgggatcc 17160
tatcaaagac caaaaaaatg agtcctgtta acaaccacct ggaacaaaaa cagattttat 17220
gcatttatgc tgctccaaga aatgctttta cgtctaagcc agaggcaatt aattaatttt 17280
tttttttttg acatggagtc actgtccgtt gcccaggctg cagtgcagtg gcgcaatctt 17340
ggctcactgc aacctccacc tcccaggttc aagtgattct cctgcctcag cctcccatgt 17400
agctgggatc acaggcacct gccaccatgc ccggctaatt ttttgtattt tttgtagaga 17460
cagggtttca ccatgttggc caggctggtc tcaaacacct gacctcaaat gatccacctg 17520
cctcagcctc ccaaagtgtt gggattacag gcgtaagcca ccatgcccag ccctgaatta 17580
atatttttaa aataagtttg gagactgttg gaaataatag ggcagaggaa catattttac 17640
tggctacttg ccagagttag ttaactcatc aaactctttg ataatagttt gacctctgtt 17700
ggtgaaaatg agccatgatc tcttgaacat gatcagaata aatgccccag ccacacaatt 17760
gtagtccaaa ctttttaggt cactaacttg ctagatggtg ccaggttttt ttgcacaagg 17820
agtgcaaatg ttaagatctc cactagtgag gaaaggctag tattacagaa gccttgtcag 17880
aggcaattga acctccaagc cctggccctc aggcctgagg attttgatac agacaaactg 17940
aagaaccgtt tgttagtgga tattgcaaac aaacaggagt caaagcttgg tgctccacag 18000
tctagttcac gagacaggcg tggcagtggc tggcagcatc tcttctcaca ggggccctca 18060
ggcacagctt accttgggag gcatgtagga agcccgctgg atcatcacgg gatacttgaa 18120
atgctcatgc aggtggtcaa catactcaca caccctagga ggagggaatc agatcggggc 18180
aatgatgcct gaagtcagat tattcacgtg gtgctaactt aaagcagaag gagcgagtac 18240
cactcaattg acagtgttgg ccaaggctta gctgtgttac catgcgtttc taggcaagtc 18300
cctaaacctc tgtgcctcag gtccttttct tctaaaatat agcaatgtga ggtggggact 18360
ttgatgacat gaacacacga agtccctctg agaggttttg tggtgccctt taaaagggat 18420
caattcagac tctgtaaata tccagaatta tttgggttcc tctggtcaaa agtcagatga 18480
atagattaaa atcaccacat tttgtgatct atttttcaag aagcgtttgt attttttcat 18540
atggctgcag cagctgccag gggcttgggg tttttttggc aggtagggtt gggagg 18596
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: d00596.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>D00596_13_142
gctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtga
gccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaa
aaaaaaaaaa
>D00596_199_328
ttttttttttttttttttgggacagtcttgctctgtcgcccaggctggagtacaatggtc
ggatcttggctcactgcaacctctgcctcccaggttcaagcaattcttctgcctcagcct
cccaagtagc
>D00596_12128_12301
agaggatttttttttttttttttttttttgagacagagttttgctctgttgcccaggctg
gaatgcaacggcgtgatcttggctcactgtaacctctgcctcctgggttcgagtgattct
cctgcctcagcctccaagtagctgggattacagcatgtgccaccatgcctggct
>D00596_12573_12749
agccaggtgtggtggctcacacctgtaattccaacaactccagaggccaaggcgagagga
tcatttgaacccacggaatttgaggctgtagtgagtcatgatcacgccattgcactccat
cctgggcaacagagtgagaccctgaatatttaaaaacaacaacaacaacaaaactct
>D00596_12246_12296
ctcctgcctcagcctccaagtagctgggattacagcatgtgccaccatgcc
>D00596_13886_13938
ggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggag
>D00596_13884_13949
tgggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaatt
gcttga
>D00596_14628_14692
tcaagcaattcttctgcctcagcctcccaggtagctgggattacaggcacatgccaccac
accca
</pre>
</td></tr></table><p>
<p><h3>File: d00596.inv</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
D00596: Score 236: 108/130 ( 83%) matches, 0 gaps
13 gctacgcgagaggctgaggcagcagaattacttgaacccaggaggcggaggttgcagtgagccgagatcgcgccactgcactccagcctgggtgagagagcgagactctgtctcaaaaaaaaaaaaaaaa 142
||||| | ||||||||||||| |||||| |||||||| |||||| |||||||||||||||| ||||| ||| || ||||||||||||| || ||||| ||||| | | ||||||||||||||||
328 cgatgaaccctccgactccgtcttcttaacgaacttggaccctccgtctccaacgtcactcggttctaggctggtaacatgaggtcggacccgctgtctcgttctgacagggtttttttttttttttttt 199
D00596: Score 164: 128/174 ( 73%) matches, 3 gaps
12128 agaggatttttttttttttttttttttttgagacagagttttgctctgttgcccaggctggaatgcaacggcgtgatcttggctcactgtaacctctgcctcc-tgggttcgagtgattctcctgcctcagcctc-caagtagctgggattaca-gcatgtgccaccatgcctggct 12301
|||| || || || || || ||||| | ||| || | |||||||||||||| |||| ||||| ||||||||| || |||||| | |||| ||| ||||||| | |||| ||| |||| ||||| ||| | ||| |||||| | || ||||||| |||||||
12749 tctcaaaacaacaacaacaacaaaaatttataagtcccagagtgagacaacgggtcctacctcacgttaccgcactagtactgagtgatgtcggagtttaaggcacccaagtttactaggagagcggaaccggagacctcaacaaccttaatgtccacactcggtggtgtggaccga 12573
D00596: Score 80: 44/51 ( 86%) matches, 2 gaps
12246 ctcctgcctcag-cctccaagtagctgggattaca-gcatgtgccaccatgcc 12296
|||||| ||||| | ||||| |||||||||||| ||||| |||||||| ||
13938 gaggacagagtcagaaggtttcacgaccctaatgtccgtactcggtggtatgg 13886
D00596: Score 99: 53/65 ( 81%) matches, 1 gaps
13884 tgggtatggtggctcatgcctgtaatcccagcactttggaagactgagacaggagcaattgcttga 13949
||||| ||||||| |||||||||||||||| ||| || ||||| ||| || ||||||||||
14692 acccacaccaccgtacacggacattagggtcgatggaccctccgactccgtcttc-ttaacgaact 14628
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
Sometimes you can find repeats using the program <b>palindrome</b> that
you can't find with <b>einverted</b> using the default parameters.
<p>
This is not due to a problem with either program. It is simply because
some of the shortest repeats that you find with <b>palindrome</b>'s
default parameter values are below <b>einverted</b>'s default cutoff
score - you should decrease the 'Minimum score threshold' to see them.
<p>
For example, when <b>palindrome</b> is run with 'em:hsfau1',
it finds the repeat:
<p>
<pre>
64 aaaactaaggc 74
|||||||||||
98 ttttgattccg 88
</pre>
<p>
<b>einverted</b> will not report this as its score is 33 (11 bases
scoring 3 each, no mismatches or gaps) with is below the default score
cutoff of 50.
<p>
If <b>einverted</b> is run as:
<p>
% einverted em:hsfau1 -threshold 33
<p>
then it will find it:
<p>
<pre>
Score 33: 11/11 (100%) matches, 0 gaps
64 aaaactaaggc 74
|||||||||||
98 ttttgattccg 88
</pre>
<p>
Anything can be considered to be a repeat if you set the score
threshold low enough!
<p>
<b>einverted</b> does not report overlapping matches.
<p>
The original "inverted" program was written to annotate the nematode
genome. Excluding overlapping repeats saved problems with simple repeat
sequences in this genome.
<H2>
References
</H2>
Some useful references on inverted repeats:
<p>
<ol>
<li>
Pearson CE, Zorbas H, Price GB, Zannis-Hadjopoulos M Inverted repeats,
stem-loops, and cruciforms: significance for initiation of DNA
replication. J Cell Biochem 1996 Oct;63(1):1-22
<li>
Waldman AS, Tran H, Goldsmith EC, Resnick MA. q Long inverted repeats
are an at-risk motif for recombination in mammalian cells.
Genetics. 1999 Dec;153(4):1873-83. PMID: 10581292; UI: 20050682
<li>
Jacobsen SE
Gene silencing: Maintaining methylation patterns.
Curr Biol 1999 Aug 26;9(16):R617-9
<li>
Lewis S, Akgun E, Jasin M.
Palindromic DNA and genome stability. Further studies.
Ann N Y Acad Sci. 1999 May 18;870:45-57.
PMID: 10415472; UI: 99343961
<li>
Dai X, Greizerstein MB, Nadas-Chinni K, Rothman-Denes LB
Supercoil-induced extrusion of a regulatory DNA hairpin. Proc Natl
Acad Sci U S A 1997 Mar 18;94(6):2174-9
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with a status of 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="equicktandem.html">equicktandem</a></td>
<td>Finds tandem repeats</td>
</tr>
<tr>
<td><a href="etandem.html">etandem</a></td>
<td>Looks for tandem repeats in a nucleotide sequence</td>
</tr>
<tr>
<td><a href="palindrome.html">palindrome</a></td>
<td>Looks for inverted repeats in a nucleotide sequence</td>
</tr>
</table>
<b>palindrome</b> also looks for inverted repeats but is much faster
and less sensitive, as it looks for near-perfect repeats.
<H2>
Author(s)
</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>
Written (1999) - Peter Rice
<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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