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An optimal method for DNA sequencing...

Heath, Samuel Aaron.

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An optimal method for DNA sequencing by hybridization.

Record Type:	Electronic resources : Monograph/item
Title/Author:	An optimal method for DNA sequencing by hybridization./
Author:	Heath, Samuel Aaron.
Description:	248 p.
Notes:	Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1797.
Contained By:	Dissertation Abstracts International64-04B.
Subject:	Computer Science. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3087272

An optimal method for DNA sequencing by hybridization.
Heath, Samuel Aaron.

An optimal method for DNA sequencing by hybridization. - 248 p.

Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1797.

Thesis (Ph.D.)--Brown University, 2003.

Sequencing by Hybridization (SBH) is a potentially powerful method for sequencing unknown DNA. An information-theoretic argument indicates that SBH can be used to sequence DNA fragments orders of magnitude longer than existing methods. Although originally proposed in 1988, SBH was unable to fulfill its promise until recently, with the invention of <italic>gapped probes</italic> containing biochemical wildcard nucleotides called <italic> universal bases</italic>. Using gapped probes and novel algorithms exploiting their structure, SBH performance has been able to formally approach the theoretic bound. This research is concerned with the development, analysis and refinement of algorithms which push performance closer to the bound, for randomly generated and natural DNA sequences.Subjects--Topical Terms:

626642
Computer Science.

An optimal method for DNA sequencing by hybridization.
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008 130614s2003 eng d
035 $a (UnM)AAI3087272
035 $a AAI3087272
040 $a UnM $c UnM
100 1 $a Heath, Samuel Aaron. $3 1940764
245 1 0 $a An optimal method for DNA sequencing by hybridization.
300 $a 248 p.
500 $a Source: Dissertation Abstracts International, Volume: 64-04, Section: B, page: 1797.
500 $a Adviser: Franco P. Preparata.
502 $a Thesis (Ph.D.)--Brown University, 2003.
520 $a Sequencing by Hybridization (SBH) is a potentially powerful method for sequencing unknown DNA. An information-theoretic argument indicates that SBH can be used to sequence DNA fragments orders of magnitude longer than existing methods. Although originally proposed in 1988, SBH was unable to fulfill its promise until recently, with the invention of <italic>gapped probes</italic> containing biochemical wildcard nucleotides called <italic> universal bases</italic>. Using gapped probes and novel algorithms exploiting their structure, SBH performance has been able to formally approach the theoretic bound. This research is concerned with the development, analysis and refinement of algorithms which push performance closer to the bound, for randomly generated and natural DNA sequences.
520 $a We present a novel analysis of the branching behaviour of the gapped SBH algorithm, and of the two failures modes of the sequencing algorithm. We also present several enhancements to the basic gapped SBH algorithm. Two of these enhancements improve performance on random DNA, and a third is designed to identify and recover from failures which occur only in natural sequences. The aggregate result of the improvements presented is to push the overall effectiveness of the algorithm on random data to almost 2/3 of the proven theoretic bound, and to significantly reduce the gap between random and natural sequence reconstruction.
590 $a School code: 0024.
650 4 $a Computer Science. $3 626642
650 4 $a Biology, Genetics. $3 1017730
690 $a 0984
690 $a 0369
710 2 0 $a Brown University. $3 766761
773 0 $t Dissertation Abstracts International $g 64-04B.
790 1 0 $a Preparata, Franco P., $e advisor
790 $a 0024
791 $a Ph.D.
792 $a 2003
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3087272