[src]$sm = {
A => {A=>5, T=>2, C=>3, G=>1 },
T => {A=>2, T=>5, C=>1, G=>4 },
C => {A=>3, T=>1, C=>5, G=>2 },
G => {A=>1, T=>4, C=>2, G=>5 }};
$gapP = -4;
$sa = 'AATTGC';
$sb = 'AGGCT';
@sa = split('',$sa);
@sb = split('',$sb);
$saLen = @sa;
$sbLen = @sb;
print "SA = @sanSB = @sbnn";
$m = [[]]; # $m =[[],[]];
for (my $b=0 ; $b<@sb ; $b++) {
for (my $a=0 ; $a<@sa ; $a++) {
$m -> [$a][$b] = $sm -> {@sa[$a]}{@sb[$b]};
print "$m->[$a][$b] ";
}
print "n";
}
print "nnn";
[/src]
