[Biojava-l] Questions about downloading sequences from DataBanks

[Shenk.Time]

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