ParAlign.org

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ParAlign

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22 March 2005: The user interface of the service has been substantially improved and a graphical overview of the matches has been added to the results.

This site provides a service for searching public sequence databases for sequences similar to a given query sequence. Searches can provide valuable information about gene relationships, functions and structure. Very accurate and rapid searches can be carried out because this service is based on very sensitive comparison methods and is powered by a large computer cluster.

The two comparison algorithms used are called Smith-Waterman (SW) and ParAlign. The first algorithm was published by Smith and Waterman (1981) and is a well established method that finds the optimal local alignment of two sequences. It is generally regarded as the "gold standard" for sequence comparison and gives the best results. However, in ordinary implementations, it is very time-consuming. By exploiting parallel computing technology, we have made the Smith-Waterman method run about 8 times faster than normal. It is therefore called accelerated Smith-Waterman. This site features the fastest implementation published of the SW-algorithm on any general-purpose microprocessor. For more information about the new implementation see Rognes and Seeberg (2000).

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