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AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM

GANTI, MANJARI
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422

Abstract Details

2007, MS, University of Cincinnati, Engineering : Computer Engineering.
The rapid growth of genetic and genomic databases has opened a new era of research in bio-computing to find fast and cost-effective solutions. Understanding regulatory activity is a first step towards determining the functionality of a gene and hence, identification of factors called transcription factors which influence the regulatory action is gaining popularity. Researchers, working on projects like the ‘Human Genome project’ are updating the genetic databases constantly and a significant speed-up on the tasks involved in sequential DNA sequence analysis becomes essential. We have developed a fast, re-configurable, cost-effective solution to the problem of identification of transcription factors in the input DNA sequences using scalable parallelism. We have adopted a matrix similarity which grades the degree of match.The design has a time complexity of the order θ(n/k + m) where n is the length of the input DNA sequence, m is the length of the pattern, k is the complexity of the design, represented by k = ns * np * d where, ns is the number of parallel streams, np is the number of patterns and d is the degree of parallelism (number of parallel units). It demonstrates a significant speed up over the software approaches which have time complexities of the order of θ(mn). Results show that the ratio of the simulation times of the hardware and software approaches termed as ‘gain’ increases linearly with the length of the DNA sequence. Hence, our design is best suited for long sequences, which typically is the case for DNA streams.
Dr. Harold Carter (Advisor)
77 p.

Recommended Citations

Citations

  • GANTI, M. (2007). AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422

    APA Style (7th edition)

  • GANTI, MANJARI. AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM. 2007. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422.

    MLA Style (8th edition)

  • GANTI, MANJARI. "AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM." Master's thesis, University of Cincinnati, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422

    Chicago Manual of Style (17th edition)

ucin1171607422
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© 2007, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.