marscan.txt

emboss的linux版本的源代码

                                  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.

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

   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.

Usage

   Here is a sample session with marscan


% marscan 
Finds MAR/SAR sites in nucleic sequences
Input nucleotide sequence(s): tembl:u01317
Output report [hshbb.marscan]: 

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

Command line arguments

   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

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   HSHBB      standard; DNA; HUM; 73308 BP.
XX
AC   U01317; J00093; J00094; J00096; J00158; J00159; J00160; J00161; J00162;
AC   J00163; J00164; J00165; J00166; J00167; J00168; J00169; J00170; J00171;
AC   J00172; J00173; J00174; J00175; J00177; J00178; J00179; K01239; K01890;
AC   K02544; M18047; M19067; M24868; M24886;
XX
SV   U01317.1
XX
DT   19-MAR-1994 (Rel. 39, Created)
DT   31-MAR-2001 (Rel. 67, Last updated, Version 28)
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; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   62409-62631, 63482-63610
RX   MEDLINE; 74275150.
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. 71:2300-2304(1974).
XX
RN   [2]
RP   63602-63646
RX   MEDLINE; 76053173.
RA   Forget B.G., Marotta C.A., Weissman S.M., Cohen-Solal M.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. 72:3614-3618(1975).
XX
RN   [3]
RP   63593-63626
RX   MEDLINE; 77022845.
RA   Proudfoot N.J., Brownlee G.G.;
RT   "Nucleotide sequences of globin messenger RNA";
RL   Br. Med. Bull. 32:251-256(1976).
XX
RN   [4]
RP   63673-63743
RX   MEDLINE; 77114153.
RA   Proudfoot N.J., Longley J.I.;