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Bioinformatics Vol. 16 no. 7 2000
Pages 628-638
© 2000 Oxford University Press

Original Paper

Object-oriented parsing of biological databases with Python

Chenna Ramu 1,*, Christine Gemünd 1 and Toby J. Gibson 1

1 European Molecular Biological Laboratory, Meyerhofstrasse 1, Postfach 10.2209, Heidelberg, Germany

Received on December 21, 1999 ; revised on February 23, 2000 ; accepted on March 8, 2000

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 later 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.

Availability: The modules are available at http://shag.embl-heidelberg.de:8000/Biopy/

Contact: chenna{at}embl-heidelberg.de

Supplementary information: http://shag.embl-heidelberg.de:8000/Biopy/

* To whom correspondence should be addressed.


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