BackgroundPairwise 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.ResultsIn 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.ConclusionsThe 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.

Abstract. Motion tracking algorithms are widely used in computer vision related research. However, the new video standards, especially those in high resolutions, cause that current implementations, even running on modern hardware, no longer meet the needs of real-time processing. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have recently been proposed. Although they present a great potential of a GPU platform, hardly any is able to process high definition video sequences efficiently. Thus, a need arose to develop a tool being able to address the outlined problem.In this paper we present software that implements optical flow motion tracking using the Lucas-Kanade algorithm. It is also integrated with the Harris corner detector and therefore the algorithm may perform sparse tracking, i.e. tracking of the meaningful pixels only. This allows to substantially lower the computational burden of the method. Moreover, both parts of the algorithm, i.e. corner selection and tracking, are implemented on GPU and, as a result, the software is immensely fast, allowing for real-time motion tracking on videos in Full HD or even 4K format. In order to deliver the highest performance, it also supports multiple GPU systems, where it scales up very well.

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