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Improving Performance Of The Smith-Waterman Algorithm

Eliminating the shortcomings of the Smith-Waterman algorithm through applying computing acceleration technologies, thus making the algorithm produce results for the shortest period of time possible.


Accuracy requires special efforts and no industry can exist without it, because if you make a mistake, the result is doomed to failure.

Undoubtedly, biotechnology requires high accuracy of calculations and search results. But what is more significant is the processing speed.

Our customer is a leading biotechnology company that provides searchable access to all available peptide and nucleotide sequences from multiple databases turned to Azati to improve the performance of one of the critical processing algorithms.


Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith–Waterman. However, because of the computationally demanding nature of this method it is a really time-consuming process.

So Azati’s main objective was to speed up the existing algorithm while keeping the data as accurate as possible.


The client company uses a dynamic programming Smith-Waterman algorithm, which is known for producing complete local alignment matches between the query sequence and the existing database sequences. The comprehensiveness of the search results is much appreciated, especially by those conducting prior art searches.

But the searches performed by the algorithm, particularly those containing a relatively long query sequence, may be frustratingly slow and took hours to get finished.Using the Smith-Waterman algorithm meant that you sacrifice your time for the accuracy of the results.


The advancement of cloud and GPU computing, in combination with further improvements to the specialized genetic alignment search technology developed by Azati, allowed our engineering team to reduce the time required to run the Smith-Waterman queries by 30-50 times.

Therefore,the implemented changes made the inordinate delays associated with running excessively long Smith-Waterman queries a thing of a past for our client.




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