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Bioinformatics tool development and ...

Staton, Margaret E.

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Bioinformatics tool development and sequence analysis of Rosaceae family expressed sequence tags.

紀錄類型:	書目-語言資料,印刷品 : Monograph/item
正題名/作者:	Bioinformatics tool development and sequence analysis of Rosaceae family expressed sequence tags./
作者:	Staton, Margaret E.
面頁冊數:	191 p.
附註:	Adviser: Doreen Main.
Contained By:	Dissertation Abstracts International68-07B.
標題:	Biology, Bioinformatics. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3274290
ISBN:	9780549149620

Bioinformatics tool development and sequence analysis of Rosaceae family expressed sequence tags.
Staton, Margaret E.

Bioinformatics tool development and sequence analysis of Rosaceae family expressed sequence tags. - 191 p.

Adviser: Doreen Main.

Thesis (Ph.D.)--Clemson University, 2007.

Background. An international community of researchers has generated a significant number of Expressed Sequence Tags (ESTs) for the Rosaceae, an economically important plant family that includes most temperate fruits such as apple, cherry, peach, and strawberry as well as other commercially valuable members. ESTs are fragments of expressed genes that can be used for gene discovery, developing markers for mapping and cultivar improvement via marker assisted selection.

ISBN: 9780549149620Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Bioinformatics tool development and sequence analysis of Rosaceae family expressed sequence tags.
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245 1 0 $a Bioinformatics tool development and sequence analysis of Rosaceae family expressed sequence tags.
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520 $a Background. An international community of researchers has generated a significant number of Expressed Sequence Tags (ESTs) for the Rosaceae, an economically important plant family that includes most temperate fruits such as apple, cherry, peach, and strawberry as well as other commercially valuable members. ESTs are fragments of expressed genes that can be used for gene discovery, developing markers for mapping and cultivar improvement via marker assisted selection.
520 $a Description. The Genome Database for Rosaceae (GDR) was initiated to provide a curated and integrated web-based relational database for this family. I developed a key component of GDR to assemble and annotate the publicly available ESTs from the four main genera of the family ( Prunus, Malus, Fragaria, Rosa). I created both genera and family level unigenes using the software CAP3 after extensive filtering, trimming and assembly. Further analysis includes marker mining for single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) with putative primer identification, and oligo identification for potential microarray development. Functional genomics efforts are supported with sequence similarity searching against major protein and nucleotide databases, gene product ontology assignment, and protein motif identification. I deployed the entire project on the GDR with all data available for browsing, searching, and downloading.
520 $a Conclusions. The GDR and its associated EST unigene project are meeting a major need for timely annotation and curation of sequence data for the Rosaceae community. The results of my analysis highlight major genes and pathways of interest including ripening, disease resistance, and transcription factors. The easily accessible pool of annotated coding sequences should further both functional and structural genomics characterization in Rosaceae. The unigene elucidates the levels of sequence similarity shared across different plant species and the implications for resource sharing across the family. GDR can be accessed at http://www.rosaceae.org/.
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