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 <[EMAIL PROTECTED]>: > 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 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
