]> Plot CpG rich areas (EMBOSS) nucleic:cpg islands http://bioweb.pasteur.fr/docs/EMBOSS/cpgplot.html cpgplot &emboss_init; input Input section sequence sequence -- DNA [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 required Required section window Window size (-window) 100 perl " -window=$value" 2 The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter. The window is moved down the sequence and these statistics are calculated at each postition that the window is moved to. 1 acd $sequence.end shift Window shift increment (-shift) 1 perl " -shift=$value" 3 This determines the number of bases that the window is moved each time after values of the percentage CG content and the Observed frequency of CG are calculated within the window. 1 acd $window minlen Minimum length of an island (-minlen) 200 perl " -minlen=$value" 4 This sets the minimum length that a CpG island has to be before it is reported. 1 acd $sequence.end minoe Minimum observed/expected (-minoe) 0.6 perl " -minoe=$value" 5 This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported. 0. 10. minpc Minimum percentage (-minpc) 50. perl " -minpc=$value" 6 This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported. 0. 100. output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 7 This sets the name of the file holding the report of the input sequence name, CpG island parameters and the output details of any CpG islands that are found. graph graph (-graph) x11 x11 hp7470 hp7470 postscript postscript cps cps hp7580 hp7580 null null data data colourps colourps text text none none tek4107t tek4107t tekt tekt xwindows xwindows hpgl hpgl xterm xterm meta meta ps ps tek tek png png tektronics tektronics postscript perl " -graph=$value" 8 obsexp Show observed/expected threshold line (-obsexp) 1 perl ($value)? "" : " -noobsexp" 9 If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed. cg Show CpG rich regions (-cg) 1 perl ($value)? "" : " -nocg" 10 If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed. pc Show percentage line (-pc) 1 perl ($value)? "" : " -nopc" 11 If this is set to true then the graph of the percentage C plus G within a window is displayed. featout featout -- nucleotide (-featout) featout.out perl " -featout=$value" 12 File for output features featout_offormat Feature output format (-offormat) perl ($value)? " -offormat=$value" : "" embl embl gff gff swiss swiss pir pir nbrf nbrf gff 12 auto perl " -auto -stdout" 13 psresults_graph perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" *.ps metaresults_graph perl $graph eq "meta" *.meta dataresults_graph perl $graph eq "data" *.dat pngresults_graph perl $graph eq "png" *.png *.2 *.3 hpglresults_graph perl $graph =~ /hp/ *.hpgl