Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

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 imp...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch, Pawel Wojciechowski
• Keywords: Alignment Algorithms, Biometrics, BMCBI 2011, Multiple Sequence Alignment, Needleman Wunsch