How do I get a sequence from NCBI?

Besides building your very own database-driven sequence repository, most users will need to fetch sequences from public datasources. A primary source of sequence information is NCBI. From its very beginning, Biojava was able to get sequences from NCBI with wrapper objects and methods. Most recently, the implementation of the Biojavax extension brought forth some changes (for example, namespaces) and the corresponding objects and methods were modified accordingly.

This example is a very simple starting point for any user who wants to get sequence info. However, beware that NCBI is looking over your shoulder and might limit your access if you are too greedy of their bandwith. Do not use these objects/methods to build a mirror copy of GenBank…

```java import org.biojava.bio.BioException; import org.biojava.bio.symbol.SymbolList; import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; import org.biojavax.bio.seq.RichSequence;

public class NCBIFileReader {

  public static void main(String[] args) {
       
     RichSequence rs = null;
       
     GenbankRichSequenceDB grsdb = new GenbankRichSequenceDB();
     try{
   // Demonstration of use with GenBank accession number
   rs = grsdb.getRichSequence("M98343");
   System.out.println(rs.getName()+" | "+rs.getDescription());
   SymbolList sl = rs.getInternalSymbolList();
   System.out.println(sl.seqString());
           
   // Demonstration of use with GenBank GI
   rs = grsdb.getRichSequence("182086");           
   System.out.println(rs.getName()+" | "+rs.getDescription());
   sl = rs.getInternalSymbolList();
   System.out.println(sl.seqString());

     }
     catch(BioException be){
   be.printStackTrace();
   System.exit(-1);
     }
  }

} ```