You could do this using a regular expression with two capturing groups, see perlretut and perlre. There are probably lots of modules out there designed for just this sort of thing.

$ perl -le '
> $seq   = q{AAAATGGGGTAAGTGAACGGGTAA};
> $start = q{ATG};
> $stop  = q{GTG};
> ( $prot1, $prot2 ) =
>    $seq =~ m{(${start}[ACGT]*?)(${stop}[ACGT]*)};
> print qq{$prot1\n$prot2\n};'
ATGGGGTAA
GTGAACGGGTAA
$
[download]

I hope this is of use.

Cheers,

JohnGG