State of the art Smith-Waterman implementations for Cell BE Michael Farrar, None 29 September 2008 The CBESW is not the only Smith-Waterman implementation for the Cell Broadband Engine (Cell BE). The Cell BE, developed by Sony, Toshiba and IBM, is found in Sony’s PlayStation 3 (PS3). The speed reported for the CBESW on the PS3 is ~3.6 GCUPS with the ability to handle sequences less than 900 residues in length. One of the first ports of the Smith-Waterman algorithm to the Cell BE was done by IBM. The port was of Erik Lindhal’s Altivec code found in SSEARCH. This Wozniak implementation is able to handle sequences of 2000 residues in length with speeds of ~4.2 GCUPS.Another recent paper describes an Alpern implementation running on a PS3. This paper reports speeds approaching 9 GCUPS while able to handle sequences of 3000 residues in length. For optimal performance, the sequence database first needs to be sorted by sequence length.The last paper describes the port of the Striped Smith-Waterman to the Cell BE. This port achieves speeds of 12 GCUPS on a PS3 and is able to handle sequences of 32,000 residues. Sachdeva, V., Kistler, M., Speight, E. and Tzeng, T. K. (2007) Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications. In Proceedings of the 21st IEEE International Parallel and Distributed processing Symposium: Long Beach, California, March 26-30, 2007. http://www.hicomb.org/HiCOMB2007/proceedings.html. Accessed 2008 Sep 18.  Rudnicki, W. R., Jankowski, A., Modzelewski, A., Piotrowski, A., Zadrozny, A. (2008) Efficient implementation of the Smith Waterman algorithm on Cell processor. In Bioinformatics 2008 Conference: Warsaw, Poland, April 24-27, 2008.https://bioinformatics2008.icm.edu.pl/web/guest/abstracts. Accessed 2008 Sep 18. Farrar, M. S. (2008) Optimizing Smith-Waterman for the Cell Broadband Engine.http://farrar.michael.googlepages.com/smith-watermanfortheibmcellbe. Accessed 2008 Sep 18. Competing interests Author of "Optimizing Smith-Waterman for the Cell Broadband Engine."