]> PRETTYPLOT Displays aligned sequences, with colouring and boxing (EMBOSS) alignment:multiple display http://bioweb.pasteur.fr/docs/EMBOSS/prettyplot.html prettyplot &emboss_init; input Input section sequences sequences -- gapany [set of sequences] (-sequences) perl " -sequences=$value -sformat=fasta" 1 File containing a sequence alignment gapany 8 seqsfile perl 1 advanced Advanced section residuesperline Number of residues to be displayed on each line (-residuesperline) 50 perl (defined $value && $value != $vdef)? " -residuesperline=$value" : "" 2 The number of residues to be displayed on each line resbreak Residues before a space (-resbreak) acd $residuesperline perl (defined $value && $value != $vdef)? " -resbreak=$value" : "" 3 1 acd $residuesperline ccolours Colour residues by their consensus value. (-ccolours) 1 perl ($value)? "" : " -noccolours" 4 cidentity Colour to display identical residues (RED) (-cidentity) RED perl ($value && $value ne $vdef)? " -cidentity=$value" : "" 5 csimilarity Colour to display similar residues (GREEN) (-csimilarity) GREEN perl ($value && $value ne $vdef)? " -csimilarity=$value" : "" 6 cother Colour to display other residues (BLACK) (-cother) BLACK perl ($value && $value ne $vdef)? " -cother=$value" : "" 7 docolour Colour residues by table oily, amide etc. (-docolour) 0 perl ($value)? " -docolour" : "" 8 title Do not display the title (-title) 1 perl ($value)? "" : " -notitle" 9 shade shading (-shade) perl ($value)? " -shade=$value" : "" 10 Set to BPLW for normal shading <BR> so for pair = 1.5,1.0,0.5 and shade = BPLW <BR> Residues score Colour <BR> 1.5 or over....... BLACK (B) <BR> 1.0 to 1.5 ....... BROWN (P) <BR> 0.5 to 1.0 ....... WHEAT (L) <BR> under 0.5 ....... WHITE (W) <BR> The only four letters allowed are BPLW, in any order. pair Values to represent identical similar related (-pair) 1.5,1.0,0.5 perl ($value && $value ne $vdef)? " -pair=$value" : "" 11 identity Only match those which are identical in all sequences. (-identity) 0 perl (defined $value && $value != $vdef)? " -identity=$value" : "" 12 box Display prettyboxes (-box) 1 perl ($value)? "" : " -nobox" 13 boxcol Colour the background in the boxes (-boxcol) 0 perl ($value)? " -boxcol" : "" 14 boxcolval Colour to be used for background. (GREY) (-boxcolval) GREY perl ($value && $value ne $vdef)? " -boxcolval=$value" : "" 15 name Display the sequence names (-name) 1 perl ($value)? "" : " -noname" 16 maxnamelen Margin size for the sequence name. (-maxnamelen) 10 perl (defined $value && $value != $vdef)? " -maxnamelen=$value" : "" 17 number Display the residue number (-number) 1 perl ($value)? "" : " -nonumber" 18 listoptions Display the date and options used (-listoptions) 1 perl ($value)? "" : " -nolistoptions" 19 plurality Plurality check value (totweight/2) (-plurality) acd @( $(sequences.totweight) / 2) perl (defined $value && $value != $vdef)? " -plurality=$value" : "" 20 consensussection Consensus section consensus Display the consensus (-consensus) 0 perl ($value)? " -consensus" : "" 21 collision Allow collisions in calculating consensus (-collision) 1 perl ($value)? "" : " -nocollision" 22 alternative Use alternative collisions routine (-alternative) 0 perl (defined $value && $value != $vdef)? " -alternative=$value" : "" 23 Use alternative collisions routine <BR> 0) Normal collision check. (default) <BR> 1) checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. <BR> 2) If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. <BR> 3) Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. 3 matrixfile Matrix file (-matrixfile) EPAM60 EPAM290 EPAM470 EPAM110 EBLOSUM50 EPAM220 EBLOSUM62-12 EPAM400 EPAM150 EPAM330 EBLOSUM55 EPAM30 EPAM260 EBLOSUM90 EPAM440 EPAM190 EPAM370 EPAM70 EPAM480 EPAM120 EDNAMAT EPAM300 EBLOSUM60 EPAM230 EBLOSUM62 EPAM410 EPAM160 EPAM340 EBLOSUM65 EPAM40 EPAM270 EPAM450 EPAM380 EPAM80 EPAM490 EBLOSUM30 EBLOSUMN EPAM200 EPAM130 EBLOSUM35 EPAM310 EBLOSUM70 EPAM10 EPAM240 EPAM420 EPAM170 EBLOSUM75 EPAM350 EPAM280 EPAM50 EPAM460 EPAM390 EPAM90 EPAM100 EBLOSUM40 EPAM210 EPAM140 EBLOSUM45 EPAM320 EBLOSUM80 EPAM500 EPAM20 EPAM250 EPAM430 EPAM180 EBLOSUM85 EPAM360 perl ($value)? " -matrixfile=$value" : "" 24 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. showscore Print residue scores (-showscore) -1 perl (defined $value && $value != $vdef)? " -showscore=$value" : "" 25 portrait Set page to Portrait (-portrait) 0 perl ($value)? " -portrait" : "" 26 output Output section graph graph [device to be displayed on] (-graph) colourps tek4107t tekt hpgl x11 cps none xwindows tek null text meta xterm ps png hp7470 postscript data hp7580 tektronics postscript perl ($value)? " -graph=$value" : "" 27 auto perl " -auto -stdout" 28 psouput perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" || $graph eq "png" perl " -goutfile=prettyplot" 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