[Biojava-l] NCBISequenceDB getSequence failed

[Richard Holland]

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NCBISequenceDB is deprecated since 1.5 and no longer supported.

Use Gen{bank,pept}SequenceDB instead in the org.biojavax.bio.db.ncbi
package.

cheers,
Richard

Christian Köberle wrote:
> 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
> 
> 
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