]> Displays all-against-all dotplots of a set of sequences (EMBOSS) alignment:dot plots http://bioweb.pasteur.fr/docs/EMBOSS/polydot.html polydot &emboss_init; input Input section sequences sequences -- any [set of sequences] (-sequences) perl " -sequences=$value -sformat=fasta" 1 File containing a sequence alignment any 8 seqsfile perl 1 required Required section wordsize Word size (-wordsize) 6 perl " -wordsize=$value" 2 2 output Output section 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" : "" 3 gap Gap (in residues) between dotplots (-gap) 10 perl (defined $value && $value != $vdef)? " -gap=$value" : "" 4 This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output. boxit Draw a box around each dotplot (-boxit) 1 perl ($value)? "" : " -noboxit" 5 dumpfeat Dump all matches as feature files (-dumpfeat) 0 perl ($value)? " -dumpfeat" : "" 6 format format to Dump out as (-format) gff perl ($value && $value ne $vdef)? " -format=$value" : "" 7 ext Extension for feature file (-ext) gff perl ($value && $value ne $vdef)? " -ext=$value" : "" 8 auto perl " -auto -stdout" 9 psouput perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" || $graph eq "png" perl " -goutfile=polydot" 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