Re: Accessing Genbank entries via biojava

There's some sample code in the BioJava cookbook:
https://github.com/biojava/biojava-tutorial/blob/master/genomics/genebank.md

On Tue, Jul 14, 2015 at 7:11 PM, Spencer Bliven <[email protected]> wrote:

> Markus,
>
> Good to hear from you! Are you still developing scabio for your class?
>
> There has been a lot of GenBank work recently, so make sure you're using
> 4.1.0. There are definitely reader and writer classes. They should take an
> InputStream if you open an http stream. There's also a
> GenbankProxySequenceReader which can fetch from NCBI.
>
> You can also post questions like this to [email protected].
>
> Cheers,
> Spencer
>
> On Fri, Jul 10, 2015 at 5:22 PM, Markus Gumbel <[email protected]>
> wrote:
>
>> Dear Spencer,
>>
>>
>>
>> I hope you remember me: We once met in Berlin and you contributed to the
>> scabio repository. Now I have question: Is it possible with biojava4 (or 3)
>> to access Genbank sequences directly over the web? I haven’t found any
>> suitable classes in the javadocs and even Google isn’t very informative.
>> Thanks for you answer!
>>
>>
>>
>> Best,
>>
>>
>>
>> Markus
>>
>>
>>
>>
>>
>> Dr. Markus Gumbel, Professor Medical Informatics / Foreign Student
>> Advisor at the Department of Computer Science
>>
>> Mannheim University of Applied Sciences, Department of Computer
>> Science/Institute f. Medical Informatics
>>
>> Paul-Wittsack-Straße 10, D-68163 Mannheim, Germany
>>
>> Phone: +49 621 292-6246, http://mi.informatik.hs-mannheim.de/gumbel/en
>>
>>
>>
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