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Assembly and analysis of complex pla...

Iowa State University., Electrical and Computer Engineering.

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Assembly and analysis of complex plant genomes.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Assembly and analysis of complex plant genomes./
Author:	Emrich, Scott Joseph.
Description:	168 p.
Notes:	Advisers: Srinivas Aluru; Patrick S. Schnable.
Contained By:	Dissertation Abstracts International68-07B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3274894
ISBN:	9780549154914

Assembly and analysis of complex plant genomes.
Emrich, Scott Joseph.

Assembly and analysis of complex plant genomes. - 168 p.

Advisers: Srinivas Aluru; Patrick S. Schnable.

Thesis (Ph.D.)--Iowa State University, 2007.

Concurrent advances in high-throughput sequencing and assembly have led to the completion of many complex genomes. Even so, these assemblies require substantial computational resources. In this dissertation, we present a massively parallel approach that scales to thousands of processors without duplicating the biological expertise present in conventional assembly software.

ISBN: 9780549154914Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Assembly and analysis of complex plant genomes.
LDR:02414nam 2200325 a 45 001 861682
005 20100720
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020 $a 9780549154914
035 $a (UMI)AAI3274894
035 $a AAI3274894
040 $a UMI $c UMI
100 1 $a Emrich, Scott Joseph. $3 1029405
245 1 0 $a Assembly and analysis of complex plant genomes.
300 $a 168 p.
500 $a Advisers: Srinivas Aluru; Patrick S. Schnable.
500 $a Source: Dissertation Abstracts International, Volume: 68-07, Section: B, page: 4206.
502 $a Thesis (Ph.D.)--Iowa State University, 2007.
520 $a Concurrent advances in high-throughput sequencing and assembly have led to the completion of many complex genomes. Even so, these assemblies require substantial computational resources. In this dissertation, we present a massively parallel approach that scales to thousands of processors without duplicating the biological expertise present in conventional assembly software.
520 $a Additional bioinformatics techniques were required to accurately assemble the maize genome including novel repeat detection, and the resulting framework has been strongly supported by maize experimental data. More recently, this framework has been generalized for fruit fly, sorghum, soybean and environmental sequence assemblies.
520 $a Questions in plant genome analysis were also addressed. For example, we have discovered an estimated 350 "orphan" maize genes and have shown that approximately 1% of all maize genes were recently duplicated, many of which into at least two functional copies. LCM-454 sequencing is introduced and analyses that indicate this approach can discover rare, potentially tissue-specific transcripts and thousands of SNPs will be presented.
520 $a This dissertation combines high performance computing, computational biology and high-throughput sequencing for our ongoing work on the maize genome project. We conclude by describing how these contributions can be useful for any species, including non-model organisms that are unlikely to be fully sequenced.
590 $a School code: 0097.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Computer Science. $3 626642
690 $a 0715
690 $a 0984
710 2 $a Iowa State University. $b Electrical and Computer Engineering. $3 1018524
773 0 $t Dissertation Abstracts International $g 68-07B.
790 $a 0097
790 1 0 $a Aluru, Srinivas, $e advisor
790 1 0 $a Schnable, Patrick S., $e advisor
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3274894