Object-oriented parsing of biological databases with Python']Python

Motivation: While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way. Results: We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for Eater analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.