#!/usr/sbin/perl #################################################### # antigenic.pl # Author: Pedro Reche # Date: May/15/2002 # Function: Detection of antigenic determinants using Kolaskar and Tongaonkar (1990) method # # ##################################################### print "Content-Type: text/html\n\n"; print "\n"; print< if (top != self){top.location.href = location.href;} \n EOT print "\n"; print< \n MIF Bioinformatics: Tools >> PREDICTED ANTIGENIC PEPTIDES \n \n \n \n \n \n \n \n \n \n \n \n \n EOT print< \n EOT local $bin="/usr/local/bin"; local $httproot = "/var/www/Tools/icons"; local $httpdata = "/var/www/tmp"; local $gnuplot = "/usr/bin/gnuplot"; local $ppmtogif = "/usr/bin/pnmtopng"; #print <Antigenic Determinants #
#end_of_text &GetFormData; $ac = $INPUT{'name'}; $ac =~ /^([\w+.])$/; $ac = $1; $AC = $ac; $var = $^T; $ac = $ac.$var; $entry = $INPUT{'sequence'}; unless ($entry) {&ShowForm; } print<
     
     
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 Tools    >> Predicting Antigenic Peptides

PREDICTED ANTIGENIC PEPTIDES

YOUR RESULTS
EOT chop($entry); $sq=""; #put sequence in entry $ID = $INPUT{'name'}; &GetDateTime; &DoData; print "\n"; close (FILE); exit; sub DoData { $sq=$entry; $sq=~s/[^ ACDEFGHIKLMNPQRSTVWY]//g; $sq=~s/ //g; $lenseq=length($sq); print "

Your $AC sequence is $lenseq residues long

\n"; $AP{'A'}=1.064; $AP{'C'}=1.412; $AP{'D'}=0.866; $AP{'E'}=0.851; $AP{'F'}=1.091; $AP{'G'}=0.874; $AP{'H'}=1.105; $AP{'I'}=1.152; $AP{'K'}=0.930; $AP{'L'}=1.250; $AP{'M'}=0.826; $AP{'N'}=0.776; $AP{'P'}=1.064; $AP{'Q'}=1.015; $AP{'R'}=0.873; $AP{'S'}=1.012; $AP{'T'}=0.909; $AP{'V'}=1.383; $AP{'W'}=0.893; $AP{'Y'}=1.161; #STEP 2 $total=0; for ($n=0;$n<$lenseq;$n++) { $char=substr($sq,$n,1); $total+=$AP{$char}; } $aap=$total/$lenseq; $aap=sprintf "%.4f",$aap; print "

Average antigenic propensity for this protein is $aap

\n"; #STEP 1 $ymax=0; $window_width=7; $firstone=int($window_width/2)+1; $w=$firstone-1; $n=$firstone; $lastone=$lenseq-$firstone; for ($n=$firstone;$n<=$lastone;$n++) { $sum=0; for ($k=-$w;$k<=$w;$k++) { $thispos=$n+$k; $char=substr($sq,$thispos,1); $sum+=$AP{$char}; } $av[$n]=$sum/$window_width; if($av[$n]>$ymax) { $ymax=$av[$n]; } } #STEP 3 if ($aap>=1.0) { for ($n=$firstone;$n<=$lastone;$n++) { if ($av[$n]>1.0) { $par[$n]=1; } else { $par[$n]=0; } } } else { for ($n=$firstone;$n<=$lastone;$n++) { if ($av[$n]>$aap) { $par[$n]=1; } else { $par[$n]=0; } } } #STEP 4 $numinarow=0; $nagd=0; for ($n=$firstone;$n<=$lastone;$n++) { $agd[$n]=0; if ($par[$n]==1) { if($numinarow==0) { $first1=$n; } $numinarow++; } else { if ($numinarow>=7) { for($j=$first1;$j<$n;$j++) { $agd[$j]=1; } $nagd++; $agd_start[$nagd]=$first1; $agd_end[$nagd]=$n-1; } $numinarow=0; } } if ($numinarow>=7) { for($j=$first1;$j<$n;$j++) { $agd[$j]=1; } $nagd++; $agd_start[$nagd]=$first1; $agd_end[$nagd]=$n-1; } #print results # results file $res = $ac.'.txt'; open (FILE,">/tmp/$res"); for ($n=$firstone;$n<=$lastone;$n++) { print FILE "$n $av[$n] $agd[$n]\n"; } close(FILE); $im=$ac.".gif"; #gnuplot file $gpfile = $ac.'.plt'; open (FILE1,">/tmp/$gpfile"); print FILE1 "set terminal pbm color \n"; print FILE1 "set title \"AC: $AC ($lenseq bases)\"\n"; print FILE1 "set xlabel \"Sequence Number\"\n"; print FILE1 "set ylabel \"Average antigenic propensity\"\n"; print FILE1 "set label 1 \"Span $window_width\" at graph 0.98,0.93 right\n"; print FILE1 "set time \"$date1\" 5,-0.5\n"; print FILE1 "set nokey\n"; print FILE1 "plot \"/tmp/$res\" using 1:2 w lines, \\\n"; print FILE1 " \"/tmp/$res\" using 1:(\$3>0.5? $ymax : 1/0) w lines lt 0 lw 4 \n"; close(FILE1); system("$gnuplot /tmp/$gpfile | $ppmtogif 2>/dev/null > $httproot/$im"); print "

Antigenic plot for sequence $AC

\n"; print ""; print "

There are $nagd antigenic determinants in your sequence:

\n"; print ""; for ($k=1;$k<=$nagd;$k++) { $ini = $agd_start[$k] -1; $ter = $agd_end[$k] - $ini; $pep = substr($sq, $ini, $ter); print "\n"; } print "
nStart PositionSequenceEnd Position
$k$agd_start[$k] $pep $agd_end[$k]
\n"; print<

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MIF Bioinformatics   |    Molecular Immunology Foundation   |   
THIS #print "
It is now $longdate
\n"; unlink("/tmp/$res"); unlink("/tmp/$gpfile"); } sub ShowForm { print <
     
     
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 Tools    >> Predicting Antigenic Peptides

PREDICTED ANTIGENIC PEPTIDES
Antigenic Introduction Directions Software

Function

This program predicts those segments from within a protein sequence that are likely to be antigenic by eliciting an antibody response.

Method

Antigenic peptides are determined using the method of Kolaskar and Tongaonkar (1990). Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes. Segments are only reported if the have a minimum size of 8 residues. The reported accuracy of method is about 75%.

Input Data

eeee &GetDateTime; print <
Enter a short name for your sequence
Replace the example sequence with your protein sequence
Hits since June/2002 Last updated:
Developer's site here
MIF Bioinformatics   |    Molecular Immunology Foundation   |   
ffff exit; } sub GetDateTime { $date = localtime(); $now=time; @days=("Sun","Mon","Tue","Wed","Thu","Fri","Sat"); @longdays=("Sunday","Monday","Tuesday","Wednesday","Thursday","Friday","Saturday"); @month=("Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec"); @longmonth=("January","February","March","April","May","June","July","August","September","October","November","December"); ($sec,$min,$hour,$mday,$mon,$yr,$wday,$yday,$isdst) = localtime(time); if ($min < 10) {$min="0".$min; } $shorttime="$hour:$min"; $year=$yr+1900; $date1="$days[$wday] $mday $month[$mon] $year at $shorttime"; $longdate="$longdays[$wday] $mday $longmonth[$mon] $year"; $thisyear=$year; } sub GetFormData { $request_method=$ENV{'REQUEST_METHOD'}; if ($request_method eq "GET") { $form_info=$ENV{'QUERY_STRING'}; } else { $size_of_info=$ENV{'CONTENT_LENGTH'}; read(STDIN, $form_info, $size_of_info); } @key_value_pairs=split(/&/,$form_info); foreach $key_value (@key_value_pairs) { ($key,$value)=split(/=/,$key_value); $value=~ tr/+/ /; $value=~ s/%([\dA-Fa-f][\dA-Fa-f])/pack("C",hex($1))/eg; $INPUT{$key} = $value; #print "",$key," = ",$value,"
\n"; } }