How To Dynamically Access Data From Ncbi Database Using Biojava?

Question

[abhishalovers]

How to dynamically access data from NCBI database using biojava?

[Pierre Lindenbaum]

why do you need BioJava ? A simple call with java.net.URL is enough.

Answer 1

[Pavel Senin]

I am sure new Biojava (3.0+) implements some methods, but I had a good experience fetching sequences with 1.8.2 version using RichSequenceDB class http://www.biojava.org/docs/api1.8.2/org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html. You'll need to instantiate the class and use the getRichSequence("accession") method. Also, NCBI provides an advanced toolkit for Java using Axis2: http://www.ncbi.nlm.nih.gov/books/NBK55696/.

Answer 2

[jlshi.nudt]

I always use R package named as GEOquery to get data from NCBI.