]> Displays a non-overlapping wordmatch dotplot of two sequences (EMBOSS) alignment:dot plots http://bioweb.pasteur.fr/docs/EMBOSS/dotpath.html dotpath &emboss_init; input Input section asequence asequence -- any [single sequence] (-asequence) perl " -asequence=$value -sformat=fasta" 1 any 8 seqfile perl 1 bsequence bsequence [single sequence] (-bsequence) perl " -bsequence=$value -sformat=fasta" 2 acd @($(acdprotein) ? stopprotein : nucleotide) 8 required Required section wordsize Word size (-wordsize) 4 perl " -wordsize=$value" 3 2 output Output section overlaps Display the overlapping matches (-overlaps) 0 perl ($value)? " -overlaps" : "" 4 Displays the overlapping matches (in red) as well as the minimal set of non-overlapping matches boxit Draw a box around dotplot (-boxit) 1 perl ($value)? "" : " -noboxit" 5 datasection Data output section graph graph [device to be displayed on] (-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 ($value)? " -graph=$value" : "" 6 auto perl " -auto -stdout" 7 psouput perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" || $graph eq "png" perl " -goutfile=dotpath" 100 psresults perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" *.ps metaresults perl $graph eq "meta" *.meta dataresults perl $graph eq "data" *.dat pngresults perl $graph eq "png" *.png *.2 *.3