Within Sequence and SymbolList the polymer is not stored as a String. BioJava differentiates different polymer residues using Symbol objects that come from different Alphabets. In this way it is easy to tell if a sequence is DNA or RNA or something else and the 'A' symbol from DNA is not equal to the 'A' symbol from RNA. The details of Symbols, SymbolLists and Alphabets are covered here. The crucial part is there needs to be a way for a programmer to convert between the easily readable String and the BioJava Object and the reverse. To do this BioJava has Tokenizers that can read a String of text and parse it into a BioJava Sequence or SymbolList object. In the case of DNA, RNA and Protein you can do this with a single method call. The call is made to a static method from either DNATools, RNATools or ProteinTools.