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

Bibliographic Details
Main Author:	GANTI, MANJARI
Language:	English
Published:	University of Cincinnati / OhioLINK 2007
Online Access:	http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422

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spelling	ndltd-OhioLink-oai-etd.ohiolink.edu-ucin11716074222021-08-03T06:11:40Z AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM GANTI, MANJARI 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. 2007-04-04 English text University of Cincinnati / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422 http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection	NDLTD
language	English
sources	NDLTD
author	GANTI, MANJARI
spellingShingle	GANTI, MANJARI AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM
author_facet	GANTI, MANJARI
author_sort	GANTI, MANJARI
title	AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM
title_short	AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM
title_full	AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM
title_fullStr	AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM
title_full_unstemmed	AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM
title_sort	approach to accelerating transcription factors identification in dna sequences using scalable parallelism
publisher	University of Cincinnati / OhioLINK
publishDate	2007
url	http://rave.ohiolink.edu/etdc/view?acc_num=ucin1171607422
work_keys_str_mv	AT gantimanjari anapproachtoacceleratingtranscriptionfactorsidentificationindnasequencesusingscalableparallelism AT gantimanjari approachtoacceleratingtranscriptionfactorsidentificationindnasequencesusingscalableparallelism
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AN APPROACH TO ACCELERATING TRANSCRIPTION FACTORS IDENTIFICATION IN DNA SEQUENCES USING SCALABLE PARALLELISM

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