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Something like this will work, it depends how yuo are storing the info. I like hashes, so I put it in a hash. open (SEQ, "proteinfile.fasta") or die "Dang!"; my $name = <SEQ>; ($genename, $species) = $name =~ /some regex/; while (<SEQ>) { if (/>/) { $genomes{$genename_species}{'genename'} =...