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

[mark.schreiber at group.novartis.com]

Hi Sumarthi,

I don't think you will be able to perform such a complex query with the 
NCBISequenceDB class. The class is really only intended to retrieve 
sequences when you know the accession number. Your query will probably 
return several accession numbers probably over both protein and DNA.

I would suggest you perform some sort of query to retreive the accessions 
you need and iterate over them passing each one to the NCBISequenceDB's 
getSequence(String id) method.

Hope this helps,

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Sumathi Murugan" <sumathi_mm at hotmail.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
04/27/2004 10:24 AM

 
        To:     biojava-dev at biojava.org
        cc: 
        Subject:        [Biojava-dev] Hi need some help in retrieving sequences using 
NCBISequenceDB 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.

_________________________________________________________________
Surf the net and talk on the phone with Xtra JetStream @ 
http://xtra.co.nz/jetstream

_______________________________________________
biojava-dev mailing list
biojava-dev at biojava.org
http://biojava.org/mailman/listinfo/biojava-dev