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Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Jacek Blazewicz12, Wojciech Frohmberg1, Michal Kierzynka14, Erwin Pesch3 and Pawel Wojciechowski1*

Author Affiliations

1 Poznań University of Technology, Poznań, Poland

2 Institute of Bioorganic Chemistry PAS, Poznań, Poland

3 University of Siegen, Siegen, Germany

4 Poznań Supercomputing and Networking Center, Poznań, Poland

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BMC Bioinformatics 2011, 12:181  doi:10.1186/1471-2105-12-181

Published: 20 May 2011

Abstract

Background

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment.

Results

In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable.

Conclusions

The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.