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Advanced Acceleration Technologies for Biological Sequence Analyses

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There has been substantial evidence that functional and structural analyses of genes and proteins can help develop new drugs, diagnose medical conditions and find cures for diseases. However, these biological sequence analyses require large-scale computational power due to the exponential growth of genomic information. During the past two decades considerable efforts have been expended in trying to accelerate the biological sequence database search process which is the fundamental step for further analyses. Various software approaches including SIMD (Single Instruction Multiple Data) instruction, multithreading, message passing programming paradigm and I/O optimization have been employed to speed up the process on different computing platforms at different levels. Hardware techniques such as FPGA (Field Programmable Gate Arrays), GPU (Graphics Processing Unit), IBM CELL BE, DSP (Digital Signal Processors) and ASIC (Applications Specific Integrated Circuit) have also been widely used. This paper reviews relevant computing platforms, various software and hardware approaches as well as the performances they achieved in high throughput sequence database search. It demonstrates that parallelism can be exploited at different phases, granularity levels, types, software/ hardware levels and scopes. This would help researchers understand current development strategies and possible future trends such as aggregate heterogeneous systems in high performance biological sequence analysis.

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Keywords: DSP; FPGA; GPU; SIMD; Smith-waterman algorithm; biological sequence analysis; heterogeneous computing

Document Type: Research Article

Publication date: September 1, 2010

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  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
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