]> Displays a thresholded dotplot of two sequences (EMBOSS) alignment:dot plots http://bioweb.pasteur.fr/docs/EMBOSS/dotmatcher.html dotmatcher &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 advanced Advanced section windowsize window size over which to test threshhold (-windowsize) 10 perl (defined $value && $value != $vdef)? " -windowsize=$value" : "" 3 3 threshold threshold (-threshold) 23 perl (defined $value && $value != $vdef)? " -threshold=$value" : "" 4 matrixfile Matrix file (-matrixfile) EPAM60 EPAM60 EPAM290 EPAM290 EPAM470 EPAM470 EPAM110 EPAM110 EBLOSUM50 EBLOSUM50 EPAM220 EPAM220 EBLOSUM62-12 EBLOSUM62-12 EPAM400 EPAM400 EPAM150 EPAM150 EPAM330 EPAM330 EBLOSUM55 EBLOSUM55 EPAM30 EPAM30 EPAM260 EPAM260 EBLOSUM90 EBLOSUM90 EPAM440 EPAM440 EPAM190 EPAM190 EPAM370 EPAM370 EPAM70 EPAM70 EPAM480 EPAM480 EPAM120 EPAM120 EDNAMAT EDNAMAT EPAM300 EPAM300 EBLOSUM60 EBLOSUM60 EPAM230 EPAM230 EBLOSUM62 EBLOSUM62 EPAM410 EPAM410 EPAM160 EPAM160 EPAM340 EPAM340 EBLOSUM65 EBLOSUM65 EPAM40 EPAM40 EPAM270 EPAM270 EPAM450 EPAM450 EPAM380 EPAM380 EPAM80 EPAM80 EPAM490 EPAM490 EBLOSUM30 EBLOSUM30 EBLOSUMN EBLOSUMN EPAM200 EPAM200 EPAM130 EPAM130 EBLOSUM35 EBLOSUM35 EPAM310 EPAM310 EBLOSUM70 EBLOSUM70 EPAM10 EPAM10 EPAM240 EPAM240 EPAM420 EPAM420 EPAM170 EPAM170 EBLOSUM75 EBLOSUM75 EPAM350 EPAM350 EPAM280 EPAM280 EPAM50 EPAM50 EPAM460 EPAM460 EPAM390 EPAM390 EPAM90 EPAM90 EPAM100 EPAM100 EBLOSUM40 EBLOSUM40 EPAM210 EPAM210 EPAM140 EPAM140 EBLOSUM45 EBLOSUM45 EPAM320 EPAM320 EBLOSUM80 EBLOSUM80 EPAM500 EPAM500 EPAM20 EPAM20 EPAM250 EPAM250 EPAM430 EPAM430 EPAM180 EPAM180 EBLOSUM85 EBLOSUM85 EPAM360 EPAM360 perl ($value)? " -matrixfile=$value" : "" 5 This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. output Output section stretch Stretch plot (-stretch) 0 perl ($value)? " -stretch" : "" 6 Display a non-proportional graph graph graph [device to be displayed on] (-graph) colourps colourps tek4107t tek4107t tekt tekt hpgl hpgl x11 x11 cps cps none none xwindows xwindows tek tek null null text text meta meta xterm xterm ps ps png png hp7470 hp7470 postscript postscript data data hp7580 hp7580 tektronics tektronics acd @(!$(stretch)) postscript perl ($value)? " -graph=$value" : "" 7 xygraph xygraph (-xygraph) colourps colourps tek4107t tek4107t tekt tekt hpgl hpgl x11 x11 cps cps none none xwindows xwindows tek tek null null text text meta meta xterm xterm ps ps png png hp7470 hp7470 postscript postscript data data hp7580 hp7580 tektronics tektronics perl $stretch acd $stretch postscript perl ($value)? " -xygraph=$value" : "" 8 auto perl " -auto -stdout" 9 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 psresults_xygraph perl $xygraph eq "postscript" || $xygraph eq "ps" || $xygraph eq "colourps" || $xygraph eq "cps" *.ps metaresults_xygraph perl $xygraph eq "meta" *.meta dataresults_xygraph perl $xygraph eq "data" *.dat pngresults_xygraph perl $xygraph eq "png" *.png *.2 *.3 hpglresults_xygraph perl $xygraph =~ /hp/ *.hpgl