東華大學圖書館 |

Language: English

Help

回圖書館首頁

手機版館藏查詢

Back

Switch To: Labeled | MARC Mode | ISBD

Algorithms for comparison of DNA seq...

Brudno, Michael.

Linked to FindBook

Google Book

Amazon

博客來

Algorithms for comparison of DNA sequences.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Algorithms for comparison of DNA sequences./
Author:	Brudno, Michael.
Description:	127 p.
Notes:	Source: Dissertation Abstracts International, Volume: 65-09, Section: B, page: 4658.
Contained By:	Dissertation Abstracts International65-09B.
Subject:	Computer Science. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3145476
ISBN:	0496042955

Algorithms for comparison of DNA sequences.
Brudno, Michael.

Algorithms for comparison of DNA sequences. - 127 p.

Source: Dissertation Abstracts International, Volume: 65-09, Section: B, page: 4658.

Thesis (Ph.D.)--Stanford University, 2004.

To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The sequencing of several mammalian genomes necessitated the development of tools for multiple alignment of large genomes. In this dissertation we describe several algorithms for alignment of long genomic sequences.

ISBN: 0496042955Subjects--Topical Terms:

626642
Computer Science.

Algorithms for comparison of DNA sequences.
LDR:03127nmm 2200325 4500 001 1844629
005 20051017073529.5
008 130614s2004 eng d
020 $a 0496042955
035 $a (UnM)AAI3145476
035 $a AAI3145476
040 $a UnM $c UnM
100 1 $a Brudno, Michael. $3 1932818
245 1 0 $a Algorithms for comparison of DNA sequences.
300 $a 127 p.
500 $a Source: Dissertation Abstracts International, Volume: 65-09, Section: B, page: 4658.
500 $a Adviser: Serafim Batzoglou.
502 $a Thesis (Ph.D.)--Stanford University, 2004.
520 $a To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The sequencing of several mammalian genomes necessitated the development of tools for multiple alignment of large genomes. In this dissertation we describe several algorithms for alignment of long genomic sequences.
520 $a The most basic of all alignment problems is that of local alignment. In this problem one is asked to return all regions of similarity that score above a particular threshold under some distance metric. We developed CHAOS, a novel heuristic local alignment algorithm that is meant to model the evolution of non-coding regions of the genome and has been shown to perform well at alignment of very distant genomic sequences.
520 $a In the problem of global alignment one introduces an additional constraint of monotonicity; the set of similarities has to be ordered in the two sequences. We developed LAGAN, an algorithm for multiple alignment of long DNA sequences. This program was shown to correctly align exons from divergent organisms and has been used extensively by biologists over the last two years. As one example of LAGAN's use, we show the multiple alignment of human, mouse and rat genomes built using this program.
520 $a In order to overcome the limitations of local and global alignment methods, we have introduced the concept of glocal alignment, where one finds a transformation of the letters of one sequence into another (as in global alignment) while allowing for various rearrangement events (as in local alignment). An approach to this problem was implemented in the Shuffle-LAGAN program that has been shown effective at finding genomic rearrangements.
520 $a Finally we demonstrate a novel approach that uses variable length words instead of fixed length ones to find seeds - short matching words between a single sequence and a database of sequences that are used to narrow down the search space for a local alignment algorithm. We demonstrate that these words (called var-mers) result in a factor of 4 decrease in the number of spurious seeds.
590 $a School code: 0212.
650 4 $a Computer Science. $3 626642
650 4 $a Biology, Genetics. $3 1017730
690 $a 0984
690 $a 0369
710 2 0 $a Stanford University. $3 754827
773 0 $t Dissertation Abstracts International $g 65-09B.
790 1 0 $a Batzoglou, Serafim, $e advisor
790 $a 0212
791 $a Ph.D.
792 $a 2004
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3145476