
                              EMBOSS: marscan
     _________________________________________________________________
   
                                Program marscan
                                       
Function

   Finds MAR/SAR sites in nucleic sequences
   
Description

   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 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.
   
   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.
   
   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.
   
   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.
   
   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.
   
Usage

   Here is a sample session with marscan:

% marscan
marscan
Finds MAR/SAR sites in nucleic sequences
Input sequence(s): EMBL:HSHBB
Output file [hshbb.marscan]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outfile]           report     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.

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outfile]
   (Parameter 2) 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.
   Report file
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Normal genomic DNA USA.
   
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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for
   further information on report formats.
   
   By default marscan writes a GFF (Gene Feature Format) report file.
   
   The output from the above example is:
     _________________________________________________________________
   
##gff-version 2.0
##date 2002-04-04
##Type DNA HSHBB
HSHBB   marscan misc_signal     2242    2458    0.000   +       .       Sequenc
e "HSHBB.1" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 245
1" ; note "*end8bp 2458" ; note "*start16bp 2242" ; note "*end16bp 2257"
HSHBB   marscan misc_signal     17654   17730   0.000   +       .       Sequenc
e "HSHBB.2" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 177
23" ; note "*end8bp 17730" ; note "*start16bp 17654" ; note "*end16bp 17669"
HSHBB   marscan misc_signal     40956   41123   0.000   +       .       Sequenc
e "HSHBB.3" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 409
56" ; note "*end8bp 40963" ; note "*start16bp 41108" ; note "*end16bp 41123"
HSHBB   marscan misc_signal     42232   42248   0.000   +       .       Sequenc
e "HSHBB.4" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 422
32" ; note "*end8bp 42239" ; note "*start16bp 42233" ; note "*end16bp 42248"
HSHBB   marscan misc_signal     47834   47966   0.000   +       .       Sequenc
e "HSHBB.5" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 479
59" ; note "*end8bp 47966" ; note "*start16bp 47834" ; note "*end16bp 47849"
HSHBB   marscan misc_signal     65112   65146   0.000   +       .       Sequenc
e "HSHBB.6" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 651
39" ; note "*end8bp 65146" ; note "*start16bp 65112" ; note "*end16bp 65127"
HSHBB   marscan misc_signal     65947   65963   0.000   +       .       Sequenc
e "HSHBB.7" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 659
47" ; note "*end8bp 65954" ; note "*start16bp 65948" ; note "*end16bp 65963"
     _________________________________________________________________
   
Data files

   None.
   
Notes

   None.
   
References

   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
   
   The original paper on MASs/SARs is:
   
   Mirkovitch J., Mirault M-E. and Laemmli UK. Cell. 1984. Vol. 39 pp.
   223-232.
   
Warnings

   It does not check that the DNA input seequnce 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 a nucleotide sequence
   fuzznuc      Nucleic acid pattern search
   fuzztran     Protein pattern search after translation
   getorf       Finds and extracts open reading frames (ORFs)
   plotorf      Plot potential open reading frames
   showorf      Pretty output of DNA translations
   wobble       Wobble base plot
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.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
