[Biojava-l] NCBISequenceDB getSequence failed

[Christian Köberle]

Hi,

I try to download Sequences via NCBISequenceDB, but is dos not work. I
get an Error: org.biojava.bio.BioException: Could not read sequence
I try also with the 1.5 BIO-JAVA but it also not work. I found that the
BIO-JAVA start a request with on with this URL:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=nucleotide&uid=NM_000530&dopt=FASTA
the result is a XML, but BIO-JAVA expect a FASTA fil [at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)].
It looks like that NCBI has changed the API.

Christian


-- 
Christian Köberle

Max Planck Institute for Infection Biology
Department of Immunology

Campus Charité Mitte
Charitéplatz 1

10117 Berlin

Tel: +49 30 28 460 562