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marscan |
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.
% marscan marscan Finds MAR/SAR sites in nucleic sequences Input sequence(s): EMBL:HSHBB Output file [hshbb.marscan]:
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 boolean 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) |
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 + . Sequence "HSHBB.1" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 2451" ; note "*end8bp 2458" ; note "*start16bp 2242" ; note "*end16bp 2257" HSHBB marscan misc_signal 17654 17730 0.000 + . Sequence "HSHBB.2" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 17723" ; note "*end8bp 17730" ; note "*start16bp 17654" ; note "*end16bp 17669" HSHBB marscan misc_signal 40956 41123 0.000 + . Sequence "HSHBB.3" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 40956" ; note "*end8bp 40963" ; note "*start16bp 41108" ; note "*end16bp 41123" HSHBB marscan misc_signal 42232 42248 0.000 + . Sequence "HSHBB.4" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 42232" ; note "*end8bp 42239" ; note "*start16bp 42233" ; note "*end16bp 42248" HSHBB marscan misc_signal 47834 47966 0.000 + . Sequence "HSHBB.5" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 47959" ; note "*end8bp 47966" ; note "*start16bp 47834" ; note "*end16bp 47849" HSHBB marscan misc_signal 65112 65146 0.000 + . Sequence "HSHBB.6" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 65139" ; note "*end8bp 65146" ; note "*start16bp 65112" ; note "*end16bp 65127" HSHBB marscan misc_signal 65947 65963 0.000 + . Sequence "HSHBB.7" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 65947" ; note "*end8bp 65954" ; note "*start16bp 65948" ; note "*end16bp 65963"
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.
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 |
Changed output file to standard EMBOSS report format (April 2002) - Peter Rice