                                   marscan



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Function

   Finds matrix/scaffold recognition (MRS) signatures in DNA sequences

Description

   marscan finds MRS recognition signatures in DNA sequences. The MRS
   signature is associated with matrix/scaffold attachment regions
   (MARs/SARs) which are genomic elements thought to delineate the
   structural and functional organisation of the eukaryotic genome. The
   MRS is a bipartite sequence element that consists of an 8bp motif
   (AATAAYAA) and a 16 bp motif (AWWRTAANNWWGNNNC) within a 200 bp
   distance from each other, on either sense strand of the genomic DNA.
   marscan reads a DNA sequence and writes a standard EMBOSS report file
   with details of the MRS signatures identified.

Algorithm

   marscan searches for an MRS signature, that being the 8bp sequence
   (AATAAYAA) and the 16 bp sequence (AWWRTAANNWWGNNNC) within a 200 bp
   distance from each other. One mismatch is allowed in the 16 bp pattern.
   The patterns may occur on the same or different strands and can
   overlap.

   Where there are many suitable 8 bp and/or 16 bp pattern sites located
   within 200 bp of each other, then only the closest pair of 8 bp / 16 bp
   sites are reported.

   Once an MRS has been reported, no more sites will be looked for within
   200 bp of that site. This reduces (but not eliminates entirely)
   over-reporting of the clusters of MRS's that tend to occur within a
   MAR/SAR.

Usage

   Here is a sample session with marscan


% marscan
Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
Input nucleotide sequence(s): tembl:u01317
Output report [u01317.marscan]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
Version: EMBOSS:6.2.0

   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
   -rstrandshow2       boolean    Show the nucleotide strand 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 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


Input file format

   marscan reads a normal genomic DNA USA.

  Input files for usage example

   'tembl:u01317' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:u01317

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   08-NOV-2008 (Rel. 97, Last updated, Version 36)
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   DOI; 10.1073/pnas.71.6.2300.
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   DOI; 10.1073/pnas.72.9.3614.
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.;


  [Part of this file has been deleted for brevity]

     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
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, 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

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default marscan writes a GFF (Gene Feature Format) report file.

  Output files for usage example

  File: u01317.marscan

##gff-version 3
##sequence-region U01317 1 65963
#!Date 2010-01-15
#!Type DNA
#!Source-version EMBOSS 6.2.0
U01317  marscan regulatory_region       2242    2458    0.000   +       .
ID="U01317.1";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 2451";
note="*end8bp 2458";note="*start16bp 2242";note="*end16bp 2257"
U01317  marscan regulatory_region       17654   17730   0.000   +       .
ID="U01317.2";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 17723"
;note="*end8bp 17730";note="*start16bp 17654";note="*end16bp 17669"
U01317  marscan regulatory_region       40956   41123   0.000   +       .
ID="U01317.3";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 40956"
;note="*end8bp 40963";note="*start16bp 41108";note="*end16bp 41123"
U01317  marscan regulatory_region       42232   42248   0.000   +       .
ID="U01317.4";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 42232"
;note="*end8bp 42239";note="*start16bp 42233";note="*end16bp 42248"
U01317  marscan regulatory_region       47834   47966   0.000   +       .
ID="U01317.5";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 47959"
;note="*end8bp 47966";note="*start16bp 47834";note="*end16bp 47849"
U01317  marscan regulatory_region       65112   65146   0.000   +       .
ID="U01317.6";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 65139"
;note="*end8bp 65146";note="*start16bp 65112";note="*end16bp 65127"
U01317  marscan regulatory_region       65947   65963   0.000   +       .
ID="U01317.7";note="*type MAR/SAR recognition site (MRS)";note="*start8bp 65947"
;note="*end8bp 65954";note="*start16bp 65948";note="*end16bp 65963"

Data files

   None.

Notes

   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.

   marscan finds a bipartite sequence element that is unique for a large
   group of eukaryotic MARs/SARs. This MAR/SAR recognition signature (MRS)
   comprises two individual sequence elements (AATAAYAA and
   AWWRTAANNWWGNNNC) that are <200 bp apart and may be aligned on
   positioned nucleosomes in MARs. The MRS signature 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 an MRS signature is observed in the DNA
   sequence, the corresponding genomic fragment is a biochemically
   identifiable SAR.

   It it still not at all clear whether MAR/SARs are real biological
   phenomena or just experimental artefacts and 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. 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.

References

    1. The method for finding the MAR/SAR sites is described in:
       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
    2. The original paper on MARs/SARs is:
       Mirkovitch J., Mirault M-E. and Laemmli UK. Cell. 1984. Vol. 39 pp.
       223-232.
    3. A recent evaluation of methods to find MARs/SARs:
       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

Warnings

   marscan does not check whether the DNA input sequence is genomic or
   not.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   dreg             Regular expression search of nucleotide sequence(s)
   fuzznuc          Search for patterns in nucleotide sequences
   fuzztran         Search for patterns in protein sequences (translated)
   getorf           Finds and extracts open reading frames (ORFs)
   plotorf          Plot potential open reading frames in a nucleotide sequence
   showorf          Display a nucleotide sequence and translation in pretty format
   sixpack          Display a DNA sequence with 6-frame translation and ORFs
   syco             Draw synonymous codon usage statistic plot for a nucleotide
                    sequence
   tcode            Identify protein-coding regions using Fickett TESTCODE statistic
   wobble           Plot third base position variability in a nucleotide sequence

Author(s)

   Gary Williams (gwilliam (c) rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Written (Jan 2001) - Gary Williams.

   Changed output file to standard EMBOSS report format (April 2002) -
   Peter Rice

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
