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    •   BracU IR
    • School of Engineering and Computer Science (SECS)
    • Department of Computer Science and Engineering (CSE)
    • Thesis & Report, BSc (Computer Science and Engineering)
    • View Item
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    Comparative analysis of protein alignment algorithms in parallel environment using CUDA

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    Date
    2016-04-18
    Publisher
    BRAC University
    Author
    Fahim, Shadman
    Prince, Gulshan Jubaed
    Hossain, Shehabul
    Metadata
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    URI
    http://hdl.handle.net/10361/5405
    Abstract
    In bioinformatics to identify evolutionary relationships two sequences are matched to find similarity. Smith Waterman, a dynamic algorithm, is a common choice to carry out this alignment process. However, with the exponential growth of protein databases this algorithm’s time complexity increases. The demand of bioinformatics for their tasks to speed up is very high. Even a slight seed up in computation would be very helpful in the field of bioinformatics. Thus, for a lot of the scientists this algorithm might not be the first choice. In today’s world the most popular and used bioinformatics tool is the BLAST (Basic Local Alignment Tool). BLAST, similar to Smith Waterman algorithm, is an alignment algorithm for scanning proteins from protein databases. This thesis analyzes both the algorithms in a parallel environment with the help of NVIDIA GPU. For our experiments we utilized a GeForce GTX 660 NVIDIA GPU to execute both the algorithms. Experimental results show that BLAST is on average is 2.5 times faster than Smith-Waterman.
    Keywords
    Computer science and engineering; CSE
     
    Description
    This thesis report is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Computer Science and Engineering, 2016.
     
    Cataloged from PDF version of thesis report.
     
    Includes bibliographical references (page 44-45).
    Department
    Department of Computer Science and Engineering, BRAC University
     
     
     
    Collections
    • Thesis & Report, BSc (Computer Science and Engineering)

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