Hi again! Thank you very much for all of your help and really good ideas. I will try all of them and see which works best in my programm. Christoforo, you're completely right: the input file is an annotated fasta file, which I have to read line by line and analyse for Codon Usage and so on. I didn't use Bioperl for creating a seqobject but instead did all the work by myself. :-) Your wellthought objection can be clearly answered, I think. If all parts are divisible by three the entire sequenz should be also divisible by three, because it consists of parts which are divisible by three. Thanks again, Markus