marscan Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Finds matrix/scaffold recognition (MRS) signatures in DNA sequences Description 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 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 1. 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 2. The original paper on MARs/SARs is: Mirkovitch J., Mirault M-E. and Laemmli UK. Cell. 1984. Vol. 39 pp. 223-232. 3. 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 (c) 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 Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None