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<HTML>
<HEAD>
<TITLE>
EMBOSS: marscan
</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">
marscan
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Finds MAR/SAR sites in nucleic sequences
<H2>
Description
</H2>
Matrix/scaffold attachment regions (MARs/SARs) are genomic elements
thought to delineate the structural and functional organisation of the
eukaryotic genome. Originally, MARs and SARs were identified through
their ability to bind to the nuclear matrix or scaffold. Binding cannot
be assigned to a unique sequence element, but is dispersed over a region
of several hundred base pairs. These elements are found flanking a gene
or a small cluster of genes and are located often in the vicinity of
cis-regulatory sequences. This has led to the suggestion that they
contribute to higher order regulation of transcription by defining
boundaries of independently controlled chromatin domains. There is
indirect evidence to support this notion. In transgenic experiments
MARs/SARs dampen position effects by shielding the transgene from the
effects of the chromatin structure at the site of integration.
Furthermore, they may act as boundary elements for enhancers,
restricting their long range effect to only the promoters that are
located in the same chromatin domain.
<p>
<b>marscan</b> finds a bipartite sequence element that is unique for a
large group of eukaryotic MARs/SARs. This MAR/SAR recognition signature
(<b>MRS</b>) comprises two individual sequence elements that are <200 bp
apart and may be aligned on positioned nucleosomes in MARs. The MRS can
be used to correctly predict the position of MARs/SARs in plants and
animals, based on genomic DNA sequence information alone. Experimental
evidence from the analysis of >300 kb of sequence data from several
eukaryotic organisms show that wherever a MRS is observed in the DNA
sequence, the corresponding genomic fragment is a biochemically
identifiable SAR.
<p>
The MRS is a bipartite sequence element that consists of two individual
sequences of 8 (AATAAYAA) and 16 bp (AWWRTAANNWWGNNNC) within a 200 bp
distance from each other. One mismatch is allowed in the 16 bp pattern.
The patterns can occur on either strand of the DNA with respect to each
other. The 8 bp and the 16 bp sites can overlap.
<p>
Where there are many possible MRS sites caused by many 8 bp and/or 16 bp
pattern sites located within 200 bp of each other, then only the 8 bp
site and the 16 bp site that occur closest to each other are reported.
<p>
Once a MRS has been reported, no more sites will be looked for within
200 bp of that site. This reduces (but maybe will not totally
eliminate) over-reporting of the clusters of MRS's that tend to occur
within a MAR/SAR.
<p>
Not all SARs contain a MRS. Analysis of >300 kb of genomic sequence
from a variety of eukaryotic organisms shows that the MRS faithfully
predicts 80% of MARs and SARs, suggesting that at least one other type
of MAR/SAR may exist which does not contain a MRS.
<p>
It it still not at all clear whether MAR/SARs are real biological phenomena
or just experimental artefacts.
<p>
The problem of how to define and find MARs is still being actively
invetsigated. For a recent evaluation of this method and others, see
reference 3.
<H2>
Usage
</H2>
<b>Here is a sample session with marscan</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>marscan </b>
Finds MAR/SAR sites in nucleic sequences
Input nucleotide sequence(s): <b>tembl:u01317</b>
Output report [u01317.marscan]: <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)
[-outfile] report [*.marscan] File for output of MAR/SAR
recognition signature (MRS) regions. This
contains details of the MRS in normal GFF
format. The MRS consists of two recognition
sites, one of 8 bp and one of 16 bp on
either sense strand of the genomic DNA,
within 200 bp of each other.
Additional (Optional) qualifiers: (none)
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>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>[-outfile]<br>(Parameter 2)</td>
<td>File for output of MAR/SAR recognition signature (MRS) regions. This contains details of the MRS in normal GFF format. The MRS consists of two recognition sites, one of 8 bp and one of 16 bp on either sense strand of the genomic DNA, within 200 bp of each other.</td>
<td>Report output file</td>
<td><i><*></i>.marscan</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 colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>marscan</b> reads a normal genomic DNA USA.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:u01317' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:u01317</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID U01317; SV 1; linear; genomic DNA; STD; HUM; 73308 BP.
XX
AC U01317; J00093-J00094; J00096; J00158-J00175; J00177-J00179; K01239;
AC K01890; K02544; M18047; M19067; M24868; M24886;
XX
DT 19-MAR-1994 (Rel. 39, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 34)
XX
DE Human beta globin region on chromosome 11.
XX
KW allelic variation; alternate cap site; Alu repeat; beta-1 pseudogene;
KW beta-globin; delta-globin; epsilon-globin; gamma-globin; gene duplication;
KW globin; HPFH; KpnI repetitive sequence; polymorphism; promoter mutation;
KW pseudogene; repetitive sequence; RNA polymerase III; thalassemia.
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 62409-62631, 63482-63610
RX PUBMED; 4135409.
RA Marotta C.A., Forget B.G., Weissman S.M., Verma I.M., McCaffrey R.P.,
RA Baltimore D.;
RT "Nucleotide sequences of human globin messenger RNA";
RL Proc. Natl. Acad. Sci. U.S.A. 71(6):2300-2304(1974).
XX
RN [2]
RP 63602-63646
RX PUBMED; 1059150.
RA Forget B.G., Marotta C.A., Weissman S.M., Cohen-Solal M.;
RT "Nucleotide sequences of the 3'-terminal untranslated region of messenger
RT RNA for human beta globin chain";
RL Proc. Natl. Acad. Sci. U.S.A. 72(9):3614-3618(1975).
XX
RN [3]
RP 63593-63626
RX PUBMED; 788834.
RA Proudfoot N.J., Brownlee G.G.;
RT "Nucleotide sequences of globin messenger RNA";
RL Br. Med. Bull. 32(3):251-256(1976).
XX
RN [4]
RP 63673-63743
RX DOI; 10.1016/0092-8674(76)90137-9.
RX PUBMED; 1035137.
RA Proudfoot N.J., Longley J.I.;
RT "The 3' terminal sequences of human alpha and beta globin messenger RNAs:
RT comparison with rabbit globin messenger RNA";
<font color=red> [Part of this file has been deleted for brevity]</font>
aaaggggaga agaatcaaat agacgcaata aaaaatgaca cggggtatca ccactgatcc 70380
cacagaaata caaactaccg tcagagaata ctataaacac ctctacgcaa ataaactaga 70440
aaatctagaa gaaatggata aattcctcga cacatacact ctgccaagac taaaccagga 70500
agaagttgta tctctgaata gaccaataac aggctctgaa attgaggcaa taattaatag 70560
cttatcaacc aaaaaaagtc cgggaccagt aggattcata gccgaattct accagaggta 70620
caaggaggag ctggtaccat tccttctgaa actattccaa tcaatagaaa aagagggaat 70680
cctccctaac tcattttatg aggccagcat catcctgata ccaaagcctg acagagacac 70740
aacaaaaaaa gagaatgtta caccaatatc cttgatgaac atcgatgcaa aaatcctcaa 70800
taaaatactg gcaaactgaa tccagcagca catcaaaaag cttatcctcc atgatcaagt 70860
gggcttcatc cctgccatgc aaggctggtt caacatacga aatcaataaa cataatccag 70920
catataaaca gaaccaaaga cacaaaccat atgattatct caatagatgc agaaaaggcc 70980
tttgacaaaa ttcaacaatg cttcatgcta aaaactctca ataaattagg tattgatggg 71040
acatatctca aaataataag agctatctat gacaaaccca cagccaatat catactgagt 71100
ggacaaaaac tggaagcatt ccctttgaaa actggcacaa ggcagggatg ccctctctca 71160
ccactcctat tcaacatagt gttggaagtt ctggccaggg caatcaggca ggagaaggaa 71220
ataaagggca ttcaattagg aaaagaggaa ggtgaaattg tccctgtttg cagatgacat 71280
gattgtatat ctagaaaacc ccattgtctc agcccaaaat ctccttaagc tgataagcaa 71340
cttcagcaaa gtctcaggat ataaaatcag tgtgcaaaaa tcacaagtat tcctatgcac 71400
caataacaga caaacagaga gccaaatcat gagtgaactc ccattcacaa ttgcttcaaa 71460
gagaataaaa tacctaggaa tccaacttac aagggatgtg aaggacctct tcaaggagaa 71520
ctacaaacca ctgctcaatg aaataaaaga ggatacaaac aaatggaaga acattccatg 71580
cttatgggta ggaagaatca tatcgtgaaa atggtcatac tgcccaaggt aatttataga 71640
ttcaatgcca tccccatcaa gctaccaatg actttcttca cagaactgga aaaaactact 71700
ttaaagttca tatggaatca aaaaagagcc cacatcacca aggcaatcct aagccaaaag 71760
aacaaagctg gaggcatcac gctacctgac ttcaaactat actacaatgc tacggtaacc 71820
aaaacagcat ggtactggta ccaaaacaga gatctagacc aatggaacag aacagagccc 71880
tcagaaataa tgccgcatat ctacaactat ccgatctttg acaaacctga gagaaacaag 71940
caatggggaa aggattccct atttaataaa tggtgctggg aaaactggct agccatatgt 72000
agaaagctga aactggatcc ttccttacac cttatacaaa aattaattca agatggatta 72060
aagacttaaa cattagacct aaaaccataa aaaccctaga aaaaaaccta ggcaatacca 72120
ttcaggacat aggcatgggc aaggacttca tgtctaaaac accaaaacga atggcaacaa 72180
aagacaaaat ggacaaacgg gatctaatta aactaaagag cttctgcaca gctaaagaaa 72240
ctaccatcag agtgaacagg caacctacaa aatgggagaa aatttttgca atctactcat 72300
ctgacaaagg gctaatatcc agaatctaca atgaactcaa acaaatttac aagaaaaaac 72360
aaacaacccc atcaaaaagt gggcaaagga tatgaacaga cacttctcaa aagaagacat 72420
ttatgtaatc aaaaaacaca tgaaaaaatg ctcatcatca ctagccatca gagaaatgca 72480
aatcaaaacc acaatgagat accatctcac accagttaga atggcgatca ttaaaaagtc 72540
aggaaacaac aggtgctgga gaggatgtgg agaaacagga acaactttta cactgttggt 72600
gggactgtaa actagttcaa ccattgcgga agtcagtgtg gcaattcctc aggaatctag 72660
aactagaaat accatttgac ccagccatcc cattactggg tagataccca aaggattata 72720
aatcatgctg ctataaagac acatgcacac gtatgtttat tgcagcacta ttcacaatag 72780
caaagacttg gaaccaaccc aaatgtccaa caacgataga ttggattaag aaaatgtggc 72840
acatatacac catggaatac tatgcagcca taaaaaatga tgagttcatg tcctttgtag 72900
ggacatggat gaagctggaa actatcattc tcagcaaact atcacaagga caataaacca 72960
aacaccgcat gttctcactc ataggtggga attgaacaat gagaacacat ggacacatga 73020
agaggaacat cacactctgg ggactgttat ggggtggggg gcaggggcag ggatagcact 73080
aggagatata cctaatgcta aatgacgagt taatgggtgc agcacaccaa catggcacat 73140
gtatacatat ataacaaacc tgccgttgtg cacatgtacc ctaaaacttg aagtataata 73200
ataaaaaaaa gttatcctat taaaactgat ctcacacatc cgtagagcca ttatcaagtc 73260
tttctctttg aaacagacag aaatttagtg ttttctcagt cagttaac 73308
//
</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>marscan</b> writes a GFF (Gene Feature Format) report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: u01317.marscan </h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 2.0
##date 2006-07-15
##Type DNA U01317
U01317 marscan misc_signal 2242 2458 0.000 + . Sequence "U01317.1" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 2451" ; note "*end8bp 2458" ; note "*start16bp 2242" ; note "*end16bp 2257"
U01317 marscan misc_signal 17654 17730 0.000 + . Sequence "U01317.2" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 17723" ; note "*end8bp 17730" ; note "*start16bp 17654" ; note "*end16bp 17669"
U01317 marscan misc_signal 40956 41123 0.000 + . Sequence "U01317.3" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 40956" ; note "*end8bp 40963" ; note "*start16bp 41108" ; note "*end16bp 41123"
U01317 marscan misc_signal 42232 42248 0.000 + . Sequence "U01317.4" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 42232" ; note "*end8bp 42239" ; note "*start16bp 42233" ; note "*end16bp 42248"
U01317 marscan misc_signal 47834 47966 0.000 + . Sequence "U01317.5" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 47959" ; note "*end8bp 47966" ; note "*start16bp 47834" ; note "*end16bp 47849"
U01317 marscan misc_signal 65112 65146 0.000 + . Sequence "U01317.6" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 65139" ; note "*end8bp 65146" ; note "*start16bp 65112" ; note "*end16bp 65127"
U01317 marscan misc_signal 65947 65963 0.000 + . Sequence "U01317.7" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 65947" ; note "*end8bp 65954" ; note "*start16bp 65948" ; note "*end16bp 65963"
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
It does not check whether the DNA input sequence is genomic or not.
<H2>
References
</H2>
<ol>
<li>
The method for finding the MAR/SAR sites is described in:
<p>
van Drunen CM., Sewalt RGAB., Oosterling RW., Weisbeek PJ., Smeekens
SCM. and van Driel R. "A bipartite sequence element associated with
matrix/scaffold attachment regions" Nucleic Acids Research. 1999. Vol
27, No. 14, pp. 2924-2930
<li>
The original paper on MARs/SARs is:
<p>
Mirkovitch J., Mirault M-E. and Laemmli UK. Cell. 1984. Vol. 39 pp. 223-232.
<li>
A recent evaluation of methods to find MARs/SARs:
<p>
I. Liebich, J. Bode, I. Reuter and E. Wingender
"Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs)"
Nucleic Acids Research 2002, Vol. 30, No. 15 3433-3442
</ol>
<H2>
Warnings
</H2>
None
<H2>
Diagnostic Error Messages
</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="dreg.html">dreg</a></td>
<td>Regular expression search of a nucleotide sequence</td>
</tr>
<tr>
<td><a href="fuzznuc.html">fuzznuc</a></td>
<td>Nucleic acid 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="getorf.html">getorf</a></td>
<td>Finds and extracts open reading frames (ORFs)</td>
</tr>
<tr>
<td><a href="plotorf.html">plotorf</a></td>
<td>Plot potential open reading frames</td>
</tr>
<tr>
<td><a href="showorf.html">showorf</a></td>
<td>Pretty output of DNA translations</td>
</tr>
<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>
<tr>
<td><a href="syco.html">syco</a></td>
<td>Synonymous codon usage Gribskov statistic plot</td>
</tr>
<tr>
<td><a href="tcode.html">tcode</a></td>
<td>Fickett TESTCODE statistic to identify protein-coding DNA</td>
</tr>
<tr>
<td><a href="wobble.html">wobble</a></td>
<td>Wobble base plot</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
Written (Jan 2001) - Gary Williams.
<p>
Changed output file to standard EMBOSS report format (April 2002) - 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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