$TITLE

#!/usr/bin/perl use CGI; my %TEMP = ('a'=>2, 't'=>2, 'g'=>4, 'c'=>4); my $TITLE = "ACGT, melting and annealing temperature calculator"; my $CGI = CGI->new(); my $CODE = $CGI->param("code"); my $RNA = $CGI->param("rna"); my $C13 = $CGI->param("c13"); my $PROC = ''; my $result = compute_result(); my $BODY_CLASS = $MESSAGE ? " warning" : ""; print < $TITLE sabina.anzlovar.com

$TITLE EOF print <Formula used: $PROC EOF print "

$MESSAGE

\n" if $MESSAGE; print "\n"; # ---------------------------------------------------------- sub compute_result { my $code = lc($CODE); $code =~ s/[^acgtu]//gs; my $aa = scalar (@a = ($code =~ m/a/sg)); my $tt = scalar (@a = ($code =~ m/t/sg)); my $uu = scalar (@a = ($code =~ m/u/sg)); my $cc = scalar (@a = ($code =~ m/c/sg)); my $gg = scalar (@a = ($code =~ m/g/sg)); if ($RNA and $tt) { $MESSAGE .= " Sequence is RNA and contains T "; } if (not $RNA and $uu) { $MESSAGE .= " Sequence is DNA and contains U "; } my $TT = $RNA ? $uu : $tt; my $all = $aa + $TT + $cc + $gg; my $mt; if ($all < 13 or $C13) { $PROC = "(less than 13 bases): a*A + t*T + c*C + g*G"; $mt = $aa * $TEMP{'a'} + $TT * $TEMP{'t'} + $cc * $TEMP{'c'} + $gg * $TEMP{'g'}; } else { $PROC = "(more than 13 bases): 64 + (g+c-16.4)/(a+t+c+g)"; $mt = 64 + ($gg+$cc-16.4)/$all; } my ($atp, $cgp, $sump); my $ann = $mt - 5; if ($all) { $mt = sprintf "%10.4f", $mt; $ann = sprintf "%10.4f", $ann; $atp = sprintf "%10.4f", (($aa + $TT) * 100) / $all; $cgp = sprintf "%10.4f", (($cc + $gg) * 100) / $all; $sump = sprintf "%10.4f", $atp + $cgp; } else { $mt = "N/A"; $ann = "N/A"; $atp = "N/A"; $cgp = "N/A"; $sump = "N/A"; } my $rv; my $checked_rna = $RNA ? "checked " : ""; my $checked_c13 = $C13 ? "checked " : ""; $rv .= "

"; $CODE =~ s/&/&/gs; $CODE =~ s//>/gs; $rv .= <
Sequence is RNA
Force formula for less than 13 bases

EOF $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; # $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "

Base	Count
A	".($aa)."
".($RNA ?"U":"T")."	".($tt)."
T	".($tt)."
U	".($uu)."
C	".($cc)."
G	".($gg)."
Total	$all

\n"; $rv .= "

\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "\n"; $rv .= "

Result	Value	Unit
A + ".($RNA ?"U":"T")."	".($aa + $TT)."	bases
C + G	".($cc + $gg)."	bases
A - ".($RNA ?"U":"T")."	$atp	%
C - G	$cgp	%
Melting	$mt	°C
Annealing	$ann	°C

\n"; $rv .= "

"; return $rv; }