Bioperl: trying XML in biology...

Catherine Letondal
Tue, 03 Aug 1999 17:45:09 +0200


We have made some tries in XML here at Pasteur (thanks to an XML course 
by S. Bortzmeyer). 

The main idea is to first convince authors of biologicial software how XML
makes it easy to parse a program's output, and that producing
XML output is easy as well (well, as long as you are the author of the code).

That's why this page:
shows examples of softs developped locally at Pasteur, to which we have
added an '-x' option in order to have them produce an XML output (CDS, satellites).

It shows also an XMLized fasta output with a parser, just to show
that a parser in XML is very easy to write, and how it could lower the 
difficulty of parsing this kind of texts.

We have also tried to see what a genbank entry would be like in XML. This is
naive of course, for only the authors of databanks may decide about this format, but
these are mainly examples. P. Bouige has also written a converter from
Genbank to XML, that works with the DTD we have set up.

We have made also simple examples of more general objects, like Phylip trees, 
but I guess that such kinds of objects will be discussed at the Bioperl 

Catherine Letondal -- -- +33 (1) 40 61 31 91
=========== Bioperl Project Mailing List Message Footer =======
Project URL:
For info about how to (un)subscribe, where messages are archived, etc: