]> Fickett TESTCODE statistic to identify protein-coding DNA (EMBOSS) nucleic:gene finding http://bioweb.pasteur.fr/docs/EMBOSS/tcode.html tcode &emboss_init; input Input section sequence sequence -- dna [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 required Required section window Length of sliding window (-window) 200 perl " -window=$value" 2 This is the number of nucleotide bases over which the TESTCODE statistic will be performed each time. The window will then slide along the sequence, covering the same number of bases each time. 200 acd $sequence.length plot Graphical display (-plot) 0 perl ($value)? " -plot" : "" 3 On selection a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed. Sequence above the green line is coding, that below the red line is non-coding. advanced Advanced section step Stepping increment for the window (-step) 3 perl (defined $value && $value != $vdef)? " -step=$value" : "" 4 The selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive). This may be altered to increase or decrease the increment of the slide. 1 acd @($(sequence.length) - $(window)) datafile Testcode data file (-datafile) perl ($value && $value ne $vdef)? " -datafile=$value" : "" 5 The default data file is Etcode.dat and contains coding probabilities for each base. The probabilities are for both positional and compositional information. output Output section outfile outfile (-outfile) acd @(!$(plot)) perl ($value)? " -outfile=$value" : "" 6 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 perl $plot acd $plot postscript perl ($value)? " -graph=$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=tcode" 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