[Biojava-l] DAS questions

Ola Spjuth ola.spjuth at farmbio.uu.se
Mon Nov 28 12:55:51 EST 2005


Experimenting with the DAS client to retrieve proteins from uniprot I
have a few questions:

dbURL = new URL("http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/");
String seqName="Q12345";
DASSequenceDB dasDB = new DASSequenceDB(dbURL);
DASSequence dasSeq = (DASSequence) dasDB.getSequence(seqName);

gives the error:

org.biojava.bio.seq.db.IllegalIDException: Database does not contain
Q12345 as a top-level sequence

but with a browser issuing
yields the result I am looking for.

I assume I am not using DASSequenceDB and DASSequence correctly. I have
not found any JUnit tests so I have no reference code. Could someone
please assist?

On a general basis: Is the DAS client in BioJava mature? Can it handle
all the major DAS-servers for proteins/genes?



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