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

[Smithies, Russell]

Hi Sumarthi,

It might be easier using Entrez' eFetch utils then parsing the results.
As you can see, it's quite easy to construct a query:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&
term=Cetacea[Organism]%20AND%20cytb&retmax=1000 

Russell Smithies

Bioinformatics Software Developer
AgResearch Invermay
Private Bag 50034
Puddle Alley
Mosgiel
New Zealand



-----Original Message-----
From: biojava-dev-bounces at portal.open-bio.org
[mailto:biojava-dev-bounces at portal.open-bio.org] On Behalf Of Sumathi
Murugan
Sent: Tuesday, 27 April 2004 2:24 p.m.
To: biojava-dev at biojava.org
Subject: [Biojava-dev] Hi need some help in retrieving sequences
usingNCBISequenceDB class


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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