Two things spring to mind about the method you have described here to get your file data into a long string. Firstly, you can achieve the same result in one fell swoop. By unsetting the $/ variable (default input record separator, a newline on *nix) the read consumes the whole file in one go. Make the change local to a small code block to avoid affecting other i/o.

my $lines;
{
    local $/ = undef;
    $lines = <INPUT>;
}
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Secondly, there is a potential flaw in your $lines = "@lines"; because interpolating a list in double quotes puts a space character between each element whereas not in quotes doesn't. E.g.

@names = ("bill", "fred", "joe");
print "@names\n";
print @names, "\n";
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produces

bill fred joe
billfredjoe
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For your problem you should have done $lines = @lines; to avoid introducing spaces into the string that weren't in the file.

Cheers,

JohnGG