High performance bioinformatics and computational biology on general-purpose graphics processing units
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Bioinformatics and Computational Biology (BCB) is a relatively new multidisciplinary field which brings together many aspects of the fields of biology, computer science, statistics, and engineering. Bioinformatics extracts useful information from biological data and makes these more intuitive and understandable by applying principles of information sciences, while computational biology harnesses computational approaches and technologies to answer biological questions conveniently. Recent years have seen an explosion of the size of biological data at a rate which outpaces the rate of increases in the computational power of mainstream computer technologies, namely general purpose processors (GPPs). The aim of this thesis is to explore the use of off-the-shelf Graphics Processing Unit (GPU) technology in the high performance and efficient implementation of BCB applications in order to meet the demands of biological data increases at affordable cost. The thesis presents detailed design and implementations of GPU solutions for a number of BCB algorithms in two widely used BCB applications, namely biological sequence alignment and phylogenetic analysis. Biological sequence alignment can be used to determine the potential information about a newly discovered biological sequence from other well-known sequences through similarity comparison. On the other hand, phylogenetic analysis is concerned with the investigation of the evolution and relationships among organisms, and has many uses in the fields of system biology and comparative genomics. In molecular-based phylogenetic analysis, the relationship between species is estimated by inferring the common history of their genes and then phylogenetic trees are constructed to illustrate evolutionary relationships among genes and organisms. However, both biological sequence alignment and phylogenetic analysis are computationally expensive applications as their computing and memory requirements grow polynomially or even worse with the size of sequence databases. The thesis firstly presents a multi-threaded parallel design of the Smith- Waterman (SW) algorithm alongside an implementation on NVIDIA GPUs. A novel technique is put forward to solve the restriction on the length of the query sequence in previous GPU-based implementations of the SW algorithm. Based on this implementation, the difference between two main task parallelization approaches (Inter-task and Intra-task parallelization) is presented. The resulting GPU implementation matches the speed of existing GPU implementations while providing more flexibility, i.e. flexible length of sequences in real world applications. It also outperforms an equivalent GPPbased implementation by 15x-20x. After this, the thesis presents the first reported multi-threaded design and GPU implementation of the Gapped BLAST with Two-Hit method algorithm, which is widely used for aligning biological sequences heuristically. This achieved up to 3x speed-up improvements compared to the most optimised GPP implementations. The thesis then presents a multi-threaded design and GPU implementation of a Neighbor-Joining (NJ)-based method for phylogenetic tree construction and multiple sequence alignment (MSA). This achieves 8x-20x speed up compared to an equivalent GPP implementation based on the widely used ClustalW software. The NJ method however only gives one possible tree which strongly depends on the evolutionary model used. A more advanced method uses maximum likelihood (ML) for scoring phylogenies with Markov Chain Monte Carlo (MCMC)-based Bayesian inference. The latter was the subject of another multi-threaded design and GPU implementation presented in this thesis, which achieved 4x-8x speed up compared to an equivalent GPP implementation based on the widely used MrBayes software. Finally, the thesis presents a general evaluation of the designs and implementations achieved in this work as a step towards the evaluation of GPU technology in BCB computing, in the context of other computer technologies including GPPs and Field Programmable Gate Arrays (FPGA) technology.