[Biojava-l] failed to read genbank peptide file

Bruno Aranda - Dev bruno_dev at ebiointel.com
Fri Jul 30 04:09:36 EDT 2004

Welcome then to the Biojava community!

I think you have a corrupt Biojava library (biojava.jar) or maybe there
are resources missing in the classpath. What you should do is:

- Download the latest binary snapshot of Biojava from

- Check that you put all the libraries needed in the classpath:

java -cp /path/to/one/jar:/path/to/another/jar ReadGB input_file

(also you can have those jars in the CLASSPATH environment variable.

You should put the jars explained at http://biojava.org/download14.html

After reading the file successfully you will get a Sequence object... you
can try to just print the sequence name (in this case the accession
number) just using:

String seqName = seq.getName();

and there are many other (and sophisticated) possibilities, of course!

Good luck,


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