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marscan |
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Function
Finds matrix/scaffold recognition (MRS) signatures in DNA sequencesDescription
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:6.4.0.0
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. (default
-rformat gff)
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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-outfile] (Parameter 2) |
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. | (default -rformat gff) | <*>.marscan |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated report qualifiers | ||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | gff |
| -rname2 -rname_outfile |
string | Base file name | Any string | |
| -rextension2 -rextension_outfile |
string | File name extension | Any string | |
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y |
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, 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 2011-07-15 #!Type DNA #!Source-version EMBOSS 6.4.0.0 U01317 marscan regulatory_region 2242 2458 . + . 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 . + . 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 . + . 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 . + . 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 . + . 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 . + . 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 . + . 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
-
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 MARs/SARs is:
Mirkovitch J., Mirault M-E. and Laemmli UK. Cell. 1984. Vol. 39 pp. 223-232.
-
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 |
|---|---|
| checktrans | Reports STOP codons and ORF statistics of a protein |
| getorf | Finds and extracts open reading frames (ORFs) |
| jaspscan | Scans DNA sequences for transcription factors |
| plotorf | Plot potential open reading frames in a nucleotide sequence |
| showorf | Display a nucleotide sequence and translation in pretty format |
| sirna | Finds siRNA duplexes in mRNA |
| 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 |
| tfscan | Identify transcription factor binding sites in DNA sequences |
| trimest | Remove poly-A tails from nucleotide sequences |
| wobble | Plot third base position variability in a nucleotide sequence |
Author(s)
Gary Williams formerly at:MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
History
Written (Jan 2001) - Gary Williams.Changed output file to standard EMBOSS report format (April 2002) - Peter Rice