RUcore: Rutgers University Community Repository
Development of a prototype visualization approach for next-generation sequencing technologies using genome navigator framework
Descriptive
TitleInfo
Title
Development of a prototype visualization approach for next-generation sequencing technologies using genome navigator framework
Name
(type = personal)
NamePart
(type = family)
Cui
NamePart
(type = given)
Tiange
NamePart
(type = date)
1984-
DisplayForm
Tiange Cui
Role
RoleTerm
(authority = RULIB)
author
Name
(type = personal)
NamePart
(type = family)
Grigoriev
NamePart
(type = given)
Andrey
DisplayForm
Andrey Grigoriev
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
Shain
NamePart
(type = given)
Daniel H
DisplayForm
Daniel H Shain
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Lee
NamePart
(type = given)
Kwangwon
DisplayForm
Kwangwon Lee
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = corporate)
NamePart
Rutgers University
Role
RoleTerm
(authority = RULIB)
degree grantor
Name
(type = corporate)
NamePart
Camden Graduate School
Role
RoleTerm
(authority = RULIB)
school
TypeOfResource
Text
Genre
(authority = marcgt)
theses
OriginInfo
DateCreated
(qualifier = exact)
2012
DateOther
(qualifier = exact);
(type = degree)
2012-05
Place
PlaceTerm
(type = code)
xx
Language
LanguageTerm
(authority = ISO639-2b);
(type = code)
eng
Abstract
(type = abstract)
The advent of next-generation sequencing (NGS) technologies has greatly accelerated the development of the genome analysis. Sequencing efficiency has improved significantly in last decade after the sequencing of the human genome was completed. A large number of NGS platforms have been developed with incredibly lower cost and higher throughputs. Terabyte of data are generated every day along with the NGS workstation, but the pace of analyzing these data is still not satisfactory. The lag between the available data and the interpretation tools will ultimately slow the progress of NGS. In this work, I aimed to add functionality to the display of NGS data in an existing genomic visualization tool - Genome Navigator (GN). By adding new features especially for the display of NGS data, the prototype GN can be used in various sequencing projects and help researchers visualize and interpret sequencing data, while exploring interested genomic region, and validating their hypotheses. After updates, the prototype GN is able to handle large amounts of sequencing data and display thousands of read at the same time. It supports several display modes such as stacked view, condensed view, and complex view. At different zoom levels, different amounts of details are shown to the users. Moreover, several utility tools have been developed to support GN when dealing with different input formats. Several new server interface features are designed for interaction with the user. I used the real sequencing data, tested the functionalities of the improvements, and had several positive results. I expect that GN will also be useful in other NGS applications and play an important role in today’s NGS research.
Subject
(authority = RUETD)
Topic
Biology
RelatedItem
(type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
(type = RULIB)
ETD
Identifier
ETD_4036
PhysicalDescription
Form
(authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
viii, 41 p. : ill.
Note
(type = degree)
M.S.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = statement of responsibility)
by Tiange Cui
Subject
(authority = ETD-LCSH)
Topic
Genomics
Subject
(authority = ETD-LCSH)
Topic
Human gene mapping
Identifier
(type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10005600001.ETD.000064968
RelatedItem
(type = host)
TitleInfo
Title
Camden Graduate School Electronic Theses and Dissertations
Identifier
(type = local)
rucore10005600001
Location
PhysicalLocation
(authority = marcorg);
(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T3JM28MD
Genre
(authority = ExL-Esploro)
ETD graduate
Back to the top
Rights
RightsDeclaration
(ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder
(type = personal)
Name
FamilyName
Cui
GivenName
Tiange
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
(encoding = w3cdtf);
(qualifier = exact);
(point = start)
2012-05-01 12:07:32
AssociatedEntity
Name
Tiange Cui
Role
Copyright holder
Affiliation
Rutgers University. Camden Graduate School
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
Back to the top
Technical
FileSize
(UNIT = bytes)
4326912
OperatingSystem
(VERSION = 5.1)
windows xp
ContentModel
ETD
MimeType
(TYPE = file)
application/pdf
MimeType
(TYPE = container)
application/x-tar
FileSize
(UNIT = bytes)
4331520
Checksum
(METHOD = SHA1)
430130aedcad69af26c027df1cc7ef7dc03233d7
Back to the top
Statistical Profile