4TH YEAR STUDIES IN COMPUTER SCIENCE

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Dzivi Ps
psd01@student.uwa.edu.au

Entry year: 2008
Enrolment status: ?
Degree: MCompSci
Degree status: complete semester 2, 2008

Project: Sequence Alignment using Graphical Processing Units
Supervisor(s): Amitava Datta
Project status: complete semester 2, 2008


The aim of this project is to find the efficiency of using Graphical Processing Units (GPUs) for sequence alignment in bioinformatics. Sequence alignment is the procedure of comparing two or more sequences to find similar sequences of amino acids or DNA base pairs with the aid of computers. The best possible alignment or optimal alignment is then used to assess their evolutionary origin. Needleman-Wunsch global sequence alignment algorithm is used for comparing two sequences over their entire length and is based on dynamic programming. The algorithm consists of a step where calculation of a value depends on previously calculated value. The calculation step exhibits some pattern of parallelism which I will try to simulate in a new algorithm. The parallel computing scheme of the algorithm will be then implemented in GPU hardware. The optimality of using CUDA compatible GPU cards for the new designed algorithm will be studied compared to other software architectures in terms of speed.

Proposal
Dissertation 		Last update: Fri Feb 20 16:23:02 2009
For further enquiries, please contact the 4th Year Coordinator, Luigi Barone.
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School of Computer Science & Software Engineering
The University of Western Australia
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Last modified: Thu Aug 20 13:23:44 2009