Smith and Waterman algorithm

1) This algorithm gives a local match between two sequences unlike needleman and wunsch which give a global alignment.

2) This method also allows insertions and deletions.

3)This method utilizes dynamic programming and works out whether it is  possible to have an optimal alignment of any  length at any location and in any sequence.

For more on Smith and Waterman visit http://www.maths.tcd.ie/~lily/pres2/sld010.htm