MapReduce Model Using FPGA Acceleration for Chromosome Y Sequence Mapping
Also Available Domains DSP Core|Xilinx Vivado
Abstract
In this project, Divide and conquer based DNA sequencing algorithm has been proposed. Sequence alignment is the foundation of bioinformatics by a computational search through large genome sequence databases, which generally requires enormous amounts of memory and takes a long execution time. In this paper, an Optimized Smith-Waterman algorithm based on the Gotoh algorithm with an affine gap for accuracy alignment, the divide and conquer technique, and the MapReduce framework implemented to establish a parallel process. This model was implemented on Virtex 7 field programmable gate arrays (FPGAs). These techniques provide a better performance, reduce the hardware requirements, improve the accuracy, increase the computational throughput, and accelerate the alignment process for big data available in a complete Y chromosome. The hardware proposed system can achieve high performance, low time consumption 1.699 ns, and decrease FPGA utilization for big data alignments Y chromosome is used as an example.
Keywords:-. MapReduce, PHSW-DC, Gotoh, smith-waterman, Y chromosome.
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Block Diagram
Specifications
Software Requirements:
- Xilinx ISE Tool
- HDL: Verilog
Hardware Requirements:
- Microsoft® Windows XP,
- Intel® Pentium® 4 processor or Pentium 4 equivalent with SSE support
- 512 MB RAM
- 100 MB of available disk space
Learning Outcomes
- Basics of Digital Electronics
- VLSI design Flow
- Introduction to Verilog Coding
- Different modeling styles in Verilog
- Data Flow modeling
- Structural modeling
- Behavioral modeling
- Mixed level modeling
- Introduction to sequence mapping circuits
- Knowledge on types of DNA nucleotides
- Different sequence mapping algorithms
- Knowledge on smith waterman algorithm
- Applications in real time
- Xilinx ISE 14.7 for design and simulation
- Generation of Netlist
- Solution providing for real time problems
- Project Development Skills:
- Problem Analysis Skills
- Problem Solving Skills
- Logical Skills
- Designing Skills
- Testing Skills
- Debugging Skills
- Presentation Skills
- Thesis Writing Skills
Paper Publishing
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