my $regex = qr/>([\S]*)\s*.*\s([A-Za-z\s]+)/;
...
while( $fasta_sequence =~ m/$regex/igm ) {

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Why are you putting the \S character class inside a character class?   Why use the /m option when you are not using either ^ or $ in the pattern?   Why use the /i option? 

    $sequence =~ tr/[\r|\n]//d; # delete all line breaks

[download]

Why are you also deleting the [, | and ] characters?

In reply to Re: Memory Growth Problem by jwkrahn
in thread Memory Growth Problem by Robgunn

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