How do I get a subsection of a Sequence?

Given a Sequence object we might only be interested in examining the first 10 bases or we might want to get a region between two points. You might also want to print a subsequence to an OutputStream like STDOUT how could you do this?

BioJava uses a biological coordinate system for identifying bases. The first base is numbered 1 and the last base index is equal to the length of the sequence. Note that this is different from String indexing which starts at 0 and proceedes to length -1. If you attempt to access a region outside of 1…length an IndexOutOfBoundsException will occur.

Getting a Sub - Sequence

`   SymbolList symL = null;`

`   //code here to generate a SymbolList`

`   //get the first Symbol`  
`   Symbol sym = symL.symbolAt(1);`

`   //get the first three bases`  
`   SymbolList symL2 = symL.subList(1,3);`

`   //get the last three bases`  
`   SymbolList symL3 = symL.subList(symL.length() - 3, symL.length());`

Printing a Sub - Sequence

`   //print the last three bases of a SymbolList or Sequence`  
`   String s = symL.subStr(symL.length() - 3, symL.length());`  
`   System.out.println(s);`

Complete Listing

```java import*; import*;

public class SubSequencing {

 public static void main(String[] args) {
   SymbolList symL = null;

   //generate an RNA SymbolList
   try {
     symL = RNATools.createRNA("auggcaccguccagauu");
   catch (IllegalSymbolException ex) {

   //get the first Symbol
   Symbol sym = symL.symbolAt(1);

   //get the first three bases
   SymbolList symL2 = symL.subList(1,3);

   //get the last three bases
   SymbolList symL3 = symL.subList(symL.length() - 3, symL.length());

   //print the last three bases
   String s = symL.subStr(symL.length() - 3, symL.length());

} ```