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G-PAS 2.0 - an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs

100%

Frohmberg W. , Kierzynka M. , Blazewicz J. , Wojciechowski P.

tom Vol. 60, nr 3

491-494

Several highly efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units). G-PAS (GPU-based Pairwise Alignment Software) was one of them, however, with a couple of interesting features that made it unique. Nevertheless, in order to adapt it to a new computational architecture some changes had to be introduced. In this paper we present G-PAS 2.0 - a new version of the software for performing high-throughput alignment. Results show, that the new version is faster nearly by a fourth on the same hardware, reaching over 20 GCUPS (Giga Cell Updates Per Second).

DNA sequence assembly involving an acyclic graph model

75%

Blazewicz J. , Frohmberg W. , Gawron P. , Kasprzak M. , Kierzynka M. , Swiercz A. , Wojciechowski P.

Foundations of Computing and Decision Sciences

2013

tom Vol. 38, No. 1

25--34

The problem of DNA sequence assembly is well known for its high complexity. Experimental errors of different kinds present in data and huge sizes of the problem instances make this problem very hard to solve. In order to deal with such data, advanced efficient heuristics must be constructed. Here, we propose a new approach to the sequence assembly problem, modeled as the problem of searching for paths in an acyclic digraph. Since the graph representing an assembly instance is not acyclic in general, it is heuristically transformed into the acyclic form. This approach reduces the time of computations significantly and allows to maintain high quality of produced solutions.