while (my $line = <INFILE> && $line !~ /SEQ.../)
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I'm usually suspicious of "my" inside conditionals. In this case, your code won't even compile under strict as you are trying to assign the value of

<INFILE> && $line !~ /SEQ.../
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to my $line.

Update: Your new version doesn't fix the problem:

while ((my $line = <INFILE>) && ($line !~ /SEQ.../))
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still produces:

Global symbol "$line" requires explicit package name
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because my doesn't declare a variable until the end of the statement that it occurs in (as I understand it).

                - tye