marscan.txt

emboss的linux版本的源代码

  [Part of this file has been deleted for brevity]

     aaaggggaga agaatcaaat agacgcaata aaaaatgaca cggggtatca ccactgatcc     7038
0
     cacagaaata caaactaccg tcagagaata ctataaacac ctctacgcaa ataaactaga     7044
0
     aaatctagaa gaaatggata aattcctcga cacatacact ctgccaagac taaaccagga     7050
0
     agaagttgta tctctgaata gaccaataac aggctctgaa attgaggcaa taattaatag     7056
0
     cttatcaacc aaaaaaagtc cgggaccagt aggattcata gccgaattct accagaggta     7062
0
     caaggaggag ctggtaccat tccttctgaa actattccaa tcaatagaaa aagagggaat     7068
0
     cctccctaac tcattttatg aggccagcat catcctgata ccaaagcctg acagagacac     7074
0
     aacaaaaaaa gagaatgtta caccaatatc cttgatgaac atcgatgcaa aaatcctcaa     7080
0
     taaaatactg gcaaactgaa tccagcagca catcaaaaag cttatcctcc atgatcaagt     7086
0
     gggcttcatc cctgccatgc aaggctggtt caacatacga aatcaataaa cataatccag     7092
0
     catataaaca gaaccaaaga cacaaaccat atgattatct caatagatgc agaaaaggcc     7098
0
     tttgacaaaa ttcaacaatg cttcatgcta aaaactctca ataaattagg tattgatggg     7104
0
     acatatctca aaataataag agctatctat gacaaaccca cagccaatat catactgagt     7110
0
     ggacaaaaac tggaagcatt ccctttgaaa actggcacaa ggcagggatg ccctctctca     7116
0
     ccactcctat tcaacatagt gttggaagtt ctggccaggg caatcaggca ggagaaggaa     7122
0
     ataaagggca ttcaattagg aaaagaggaa ggtgaaattg tccctgtttg cagatgacat     7128
0
     gattgtatat ctagaaaacc ccattgtctc agcccaaaat ctccttaagc tgataagcaa     7134
0
     cttcagcaaa gtctcaggat ataaaatcag tgtgcaaaaa tcacaagtat tcctatgcac     7140
0
     caataacaga caaacagaga gccaaatcat gagtgaactc ccattcacaa ttgcttcaaa     7146
0
     gagaataaaa tacctaggaa tccaacttac aagggatgtg aaggacctct tcaaggagaa     7152
0
     ctacaaacca ctgctcaatg aaataaaaga ggatacaaac aaatggaaga acattccatg     7158
0
     cttatgggta ggaagaatca tatcgtgaaa atggtcatac tgcccaaggt aatttataga     7164
0
     ttcaatgcca tccccatcaa gctaccaatg actttcttca cagaactgga aaaaactact     7170
0
     ttaaagttca tatggaatca aaaaagagcc cacatcacca aggcaatcct aagccaaaag     7176
0
     aacaaagctg gaggcatcac gctacctgac ttcaaactat actacaatgc tacggtaacc     7182
0
     aaaacagcat ggtactggta ccaaaacaga gatctagacc aatggaacag aacagagccc     7188
0
     tcagaaataa tgccgcatat ctacaactat ccgatctttg acaaacctga gagaaacaag     7194
0
     caatggggaa aggattccct atttaataaa tggtgctggg aaaactggct agccatatgt     7200
0
     agaaagctga aactggatcc ttccttacac cttatacaaa aattaattca agatggatta     7206
0
     aagacttaaa cattagacct aaaaccataa aaaccctaga aaaaaaccta ggcaatacca     7212
0
     ttcaggacat aggcatgggc aaggacttca tgtctaaaac accaaaacga atggcaacaa     7218
0
     aagacaaaat ggacaaacgg gatctaatta aactaaagag cttctgcaca gctaaagaaa     7224
0
     ctaccatcag agtgaacagg caacctacaa aatgggagaa aatttttgca atctactcat     7230
0
     ctgacaaagg gctaatatcc agaatctaca atgaactcaa acaaatttac aagaaaaaac     7236
0
     aaacaacccc atcaaaaagt gggcaaagga tatgaacaga cacttctcaa aagaagacat     7242
0
     ttatgtaatc aaaaaacaca tgaaaaaatg ctcatcatca ctagccatca gagaaatgca     7248
0
     aatcaaaacc acaatgagat accatctcac accagttaga atggcgatca ttaaaaagtc     7254
0
     aggaaacaac aggtgctgga gaggatgtgg agaaacagga acaactttta cactgttggt     7260
0
     gggactgtaa actagttcaa ccattgcgga agtcagtgtg gcaattcctc aggaatctag     7266
0
     aactagaaat accatttgac ccagccatcc cattactggg tagataccca aaggattata     7272
0
     aatcatgctg ctataaagac acatgcacac gtatgtttat tgcagcacta ttcacaatag     7278
0
     caaagacttg gaaccaaccc aaatgtccaa caacgataga ttggattaag aaaatgtggc     7284
0
     acatatacac catggaatac tatgcagcca taaaaaatga tgagttcatg tcctttgtag     7290
0
     ggacatggat gaagctggaa actatcattc tcagcaaact atcacaagga caataaacca     7296
0
     aacaccgcat gttctcactc ataggtggga attgaacaat gagaacacat ggacacatga     7302
0
     agaggaacat cacactctgg ggactgttat ggggtggggg gcaggggcag ggatagcact     7308
0
     aggagatata cctaatgcta aatgacgagt taatgggtgc agcacaccaa catggcacat     7314
0
     gtatacatat ataacaaacc tgccgttgtg cacatgtacc ctaaaacttg aagtataata     7320
0
     ataaaaaaaa gttatcctat taaaactgat ctcacacatc cgtagagcca ttatcaagtc     7326
0
     tttctctttg aaacagacag aaatttagtg ttttctcagt cagttaac                  7330
8
//

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, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, 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: hshbb.marscan

##gff-version 2.0
##date 2006-07-15
##Type DNA HSHBB
HSHBB   marscan misc_signal     2242    2458    0.000   +       .       Sequenc
e "HSHBB.1" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 245
1" ; note "*end8bp 2458" ; note "*start16bp 2242" ; note "*end16bp 2257"
HSHBB   marscan misc_signal     17654   17730   0.000   +       .       Sequenc
e "HSHBB.2" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 177
23" ; note "*end8bp 17730" ; note "*start16bp 17654" ; note "*end16bp 17669"
HSHBB   marscan misc_signal     40956   41123   0.000   +       .       Sequenc
e "HSHBB.3" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 409
56" ; note "*end8bp 40963" ; note "*start16bp 41108" ; note "*end16bp 41123"
HSHBB   marscan misc_signal     42232   42248   0.000   +       .       Sequenc
e "HSHBB.4" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 422
32" ; note "*end8bp 42239" ; note "*start16bp 42233" ; note "*end16bp 42248"
HSHBB   marscan misc_signal     47834   47966   0.000   +       .       Sequenc
e "HSHBB.5" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 479
59" ; note "*end8bp 47966" ; note "*start16bp 47834" ; note "*end16bp 47849"
HSHBB   marscan misc_signal     65112   65146   0.000   +       .       Sequenc
e "HSHBB.6" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 651
39" ; note "*end8bp 65146" ; note "*start16bp 65112" ; note "*end16bp 65127"
HSHBB   marscan misc_signal     65947   65963   0.000   +       .       Sequenc
e "HSHBB.7" ; note "*type MAR/SAR recognition site (MRS)" ; note "*start8bp 659
47" ; note "*end8bp 65954" ; note "*start16bp 65948" ; note "*end16bp 65963"

Data files

   None.

Notes

   It does not check whether the DNA input sequence is genomic or not.

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

   None

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   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
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   syco         Synonymous codon usage Gribskov statistic plot
   tcode        Fickett TESTCODE statistic to identify protein-coding DNA
   wobble       Wobble base plot

Author(s)

   Gary Williams (gwilliam