[Biojava-dev] Hi need some help in retrieving sequences using NCBISequenceDB class

[Sumathi Murugan]

Hi everyone,

     i am  quite new to bioinformatics field. i want  to retrieve all the 
Sequences related to some Query (Organism Cetacea and Cytb gene) using 
entrez.  i donot know how to retrieve those ids from NCBISequence Database. 
my code is



import java.io.*;
import java.util.*;

import org.biojava.bio.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;

public class NcbiRead {

        public static void main(String[] args) throws Exception {

                String server="http://www.ncbi.nlm.nih.gov/";
                String cgi = "entrez/Cetacea[Organism] AND cytb";
                String dBase = "nucleotide";
                GenbankFormat gf = new GenbankFormat();
                NCBISequenceDB db=new NCBISequenceDB(server,cgi,dBase,gf);

      }
}

The NCBISequenceDB has methods to retrieve sequence if user gives a 
particular id.  In my case the ids are in NCBISequenceDB. honestly i don't 
know. i will be grateful if someone help me in getting progress.

thanks in advance,
Sumathi,
Dept of BioInformatics,
Auckland,
NewZealand.

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