... Better would be while (defined (my $seq = <$IN2>)) {

AFAIK, current versions of Perl implicitly do this anyway:

#!/usr/bin/perl

open my $IN2, "<", "foo.txt" or die;

while (my $seq = <$IN2>) {
    print "line: '$seq'\n";
}
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$ perl -MO=Deparse ./808927.pl
die unless open my $IN2, '<', 'foo.txt';
while (defined(my $seq = <$IN2>)) {
    print "line: '${seq}'\n";
}
./808927.pl syntax OK
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It's only when you write things like while (chomp(my $seq = <$IN2>)) that you run into problems... (because chomp returns the number of characters removed, which may be zero for the last line if it doesn't contain a "\n")