$file = "xyz"; if(!open(READ_FILE, "$file")){ die "Cannot open file [$file]\n"; } my $sequence = ""; while(my $line = ){ if($line =~ m/^G.*\(EC/){ if($sequence){ #write sequence here. print "seq: $sequence\n"; $sequence = ""; } $sequence .= $line; }else{ $sequence .= $line; } } #write last sequence here print "last: $sequence\n";