Try
my %fasta_seen;
FASTA_RECORD:
while ( my $para = <$PROTFILE> ) {
# Remove fasta header line
if ( $para =~ s/^>(.*)//m ){
$name = $1;
};
# Remove comment line(s)
$para =~ s/^\s*#.*//mg;
next FASTA_RECORD if $fasta_seen{ $para }++;
…
This may not be a sensible solution if your sequences are very long in which case consider using a message digest like Digest::MD5
poj
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