[Biojava-l] Questions about downloading sequences from DataBanks

[Richard Holland]

Hello.

The basic way of fetching a load of sequences from eutils by
specifying a set of Genbank IDs can be done using this:

  http://biojava.org/docs/api/org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html

If you want to specify more complex queries for locating sequences
other than just by ID, you'll need to make a copy of
GenbankRichSequenceDB and modify it to allow such queries. It uses the
direct URL method for interacting with Entrez/eutils, and so with your
modified class you'll be able to do anything that the webservice can
do via URL requests.

cheers,
Richard


2008/11/7 Shenk.Time <ixiivilibra at gmail.com>:
> Hi friends!
>
> I am a preliminary learner of Biojava, and I just joined this booming
> organization some days ago. Apparently, Biojava is not a simple system,
> although there are a lot of examples on the website against so much more
> functions. Actually, the motivation of my starting to focus on it is I want
> to download sequences of genes, genomes or proteins freely and
> automatically. Gradually, with the progress of my learning, I found that it
> is a very useful tool for processing biological data. And I also like the
> conception model of biological entities expressed in Biojava. However, my
> problem still exists. I have been searching the answer for almost one month.
> It has disturbed me so much.
>
> How can I download the sequence data from NCBI or EBI freely, massively and
> automatically? Does Biojava have this function? If it does, then how can I
> do it? What Classes, Functions or packages should I learn?
>
> As I already knew, NCBI supports a kind of web service named 'eUtility'. The
> SOAP/WSDL model is recommended by them. Once, I used the Axis2 (developed by
> Apache) and the wsdl file (a URL on their website) to produce '*stub.java'
> files successfully on my computer. Because of the various versions, I had to
> produce groups of '*stub.java' files and *stub-like classes. And I have also
> tested those examples they give out. But, that is all. There is no
> documentation! It is difficult to understand how to use all the functions of
> their API by reading the source code.
>
>  So, if Biojava has no ability to solve this problem, then what should I
> do?
>
> I want to ask some help from you precursors and colleagues. Thank you very
> much!
>
>
>
> Best regards.
>
>
>
>
>
> Shenk Time
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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/