]> Finds PEST motifs as potential proteolytic cleavage sites (EMBOSS) protein:motifs http://bioweb.pasteur.fr/docs/EMBOSS/epestfind.html epestfind &emboss_init; input Input section sequence sequence -- protein [single sequence] (-sequence) perl " -sequence=$value -sformat=fasta" 1 Protein sequence USA to be analysed. protein 8 seqfile perl 1 required Required section window Window length (-window) 10 perl " -window=$value" 2 Minimal distance between positively charged amino acids. 2 acd $sequence.length order Sort order of results -- Sort order of results (-order) 1 length 2 position 3 score score perl " -order=$value" 3 Name of the output file which holds the results of the analysis. Results may be sorted by length, position and score. potential Display potential PEST motifs (-potential) 1 perl ($value)? "" : " -nopotential" 4 Decide whether potential PEST motifs should be printed. poor Display poor PEST motifs (-poor) 1 perl ($value)? "" : " -nopoor" 5 Decide whether poor PEST motifs should be printed. invalid Display invalid PEST motifs (-invalid) 0 perl ($value)? " -invalid" : "" 6 Decide whether invalid PEST motifs should be printed. map Display PEST motifs map (-map) 1 perl ($value)? "" : " -nomap" 7 Decide whether PEST motifs should be mapped to sequence. output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 8 Name of file to which results will be written. graph graph (-graph) 1 2 3 postscript perl ($value)? " -graph=$value" : "" 9 advanced Advanced section threshold Threshold score (-threshold) +5.0 perl (defined $value && $value != $vdef)? " -threshold=$value" : "" 10 Threshold value to discriminate weak from potential PEST motifs. Valid PEST motifs are discriminated into 'poor' and 'potential' motifs depending on this threshold score. By default, the default value is set to +5.0 based on experimental data. Alterations are not recommended since significance is a matter of biology, not mathematics. -55.0 +55.0 aadata Amino acid data file (-aadata) Eamino.dat perl ($value && $value ne $vdef)? " -aadata=$value" : "" 11 File of amino acid properties and molecular masses. auto perl " -auto -stdout" 12 psouput perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" || $graph eq "png" perl " -goutfile=epestfind" 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