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EMBOSS: 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:u01317 Output file [hsfau1.marscan]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outf] featout 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 |
[-outf] (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. | Writeable feature table | unknown.gff |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
The output from the above example is:
##gff-version 0.0 ##date 2001-02-21 ##sequence-region HSHBB 0 0 HSHBB marscan misc_signal 2242 2458 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=2451..2458. 16bp pattern = 2242..2257" HSHBB marscan misc_signal 17654 17730 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=17723..17730. 16bp pattern = 17654..17669" HSHBB marscan misc_signal 40956 41123 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=40956..40963. 16bp pattern = 41108..41123" HSHBB marscan misc_signal 42232 42248 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=42232..42239. 16bp pattern = 42233..42248" HSHBB marscan misc_signal 47834 47966 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=47959..47966. 16bp pattern = 47834..47849" HSHBB marscan misc_signal 65112 65146 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=65139..65146. 16bp pattern = 65112..65127" HSHBB marscan misc_signal 65947 65963 1.0 . . note "MAR/SAR recognition site (MRS). 8bp pattern=65947..65954. 16bp pattern = 65948..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 |