Tools

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001 ocn869832907;

003 OCoLC;

005 20140310011118.0;

006 m o d ;

007 cr bn|||||||||;

008 140204s2013 ncua ob 000 0 eng d;

035 a| (Sirsi) o869832907;

035 a| (OCoLC)869832907;

049 a| EREE;

090 a| QH324.2;

100 1 a| Ahmadvand, Ali,e| author.?| UNAUTHORIZED;

245 10 a| AlienG2 :b| an automated analysis tool for genome-scale prediction of horizontal gene transfer /c| by Ali Ahmadvand.;

264 1 a| [Greenville, N.C.] :b| [East Carolina University],c| 2013.;

300 a| 63 pages :b| illustrations (some color);

336 a| textb| txt2| rdacontent;

337 a| computerb| c2| rdamedia;

338 a| online resourceb| cr2| rdacarrier;

347 a| text fileb| PDFc| 1.59Mb2| rda;

538 a| System requirements: Adobe Reader.;

538 a| Mode of access: World Wide Web.;

502 b| M.S.c| East Carolina Universityd| 2013.;

500 a| Presented to the faculty of the Department of Computer Science.;

500 a| Advisor: Qin Ding.;

500 a| Title from PDF t.p. (viewed February 21, 2014).;

520 3 a| This thesis will present a method for predicting Horizontal Gene Transfer (HGT) events through the creation of a web-based application called AlienG2. HGT is the process of genetic exchange between distantly related organisms. The benefits and applications for identifying HGT are numerous and have been studied in depth, as well as the many techniques and related tools for identifying them. Each one of these tools has its own advantages and disadvantages; yet, there is still a need for a tool that may be used practically and that also delivers results in a relatively short turnaround. AlienG2 consists of the combination of two already established methods, AlienG and PhyloGenie. AlienG is a sequence similarity comparison based tool that assumes that sequence similarity is correlated to phylogenetic relatedness. Although this tool is fast, the accuracy of the result could be improved. On the other hand, however, while PhyloGenie has been developed using phylogenetic techniques and is known to be the most precise technique for identifying HGT, its very long running time makes it practically unusable. In order to create AlienG2 both AlienG and PhyloGenie had to be improved and then combined. As another improvement to make it more easily accessible for its primary users, which are mostly biologists, this tool was created with Web Service architecture and as a web-based application. The results of experiments show drastic improvement in the running time of the tool, making it quite practical.;

504 a| Includes bibliographical references.;

650 0 a| Bioinformatics.=| ^A493304;

650 0 a| Web applications.=| ^A1167535;

650 0 a| Genetic transformation.=| ^A137175;

653 a| Computer science;

653 a| Bioinformatics;

700 1 a| Ding, Qin,e| degree supervisor.=| ^A1464811;

710 2 a| East Carolina University.b| Department of Computer Science.?| UNAUTHORIZED;

856 40 z| Access via ScholarShipu| http://hdl.handle.net/10342/4295;

949 o| jgml;

994 a| C0b| ERE;

596 a| 1 4;

998 a| 3422603;

999 a| CLICK ON WEB ADDRESSw| ASISc| 1i| 3422603-1001l| JNETm| JOYNERr| Ys| Yt| JNE3ETDu| 2/4/2014x| ETDz| JERESOURCE;

999 a| CLICK ON WEB ADDRESSw| ASISc| 1i| 3422603-2001l| HSLELECm| HSLr| Ys| Yt| HEETDu| 2/4/2014x| ETDz| HERESOURCE;

AlienG2 : an automated analysis tool for genome-scale prediction of horizontal gene transfer / by Ali Ahmadvand.

Author/creator	Ahmadvand, Ali author.
Other author	Ding, Qin, degree supervisor.
Other author	East Carolina University. Department of Computer Science.
Format	Theses and dissertations
Publication	[Greenville, N.C.] : [East Carolina University], 2013.
Description	63 pages : illustrations (some color)
Supplemental Content	Access via ScholarShip
Subjects	Bioinformatics. Web applications. Genetic transformation.

Summary	This thesis will present a method for predicting Horizontal Gene Transfer (HGT) events through the creation of a web-based application called AlienG2. HGT is the process of genetic exchange between distantly related organisms. The benefits and applications for identifying HGT are numerous and have been studied in depth, as well as the many techniques and related tools for identifying them. Each one of these tools has its own advantages and disadvantages; yet, there is still a need for a tool that may be used practically and that also delivers results in a relatively short turnaround. AlienG2 consists of the combination of two already established methods, AlienG and PhyloGenie. AlienG is a sequence similarity comparison based tool that assumes that sequence similarity is correlated to phylogenetic relatedness. Although this tool is fast, the accuracy of the result could be improved. On the other hand, however, while PhyloGenie has been developed using phylogenetic techniques and is known to be the most precise technique for identifying HGT, its very long running time makes it practically unusable. In order to create AlienG2 both AlienG and PhyloGenie had to be improved and then combined. As another improvement to make it more easily accessible for its primary users, which are mostly biologists, this tool was created with Web Service architecture and as a web-based application. The results of experiments show drastic improvement in the running time of the tool, making it quite practical.
General note	Presented to the faculty of the Department of Computer Science.
General note	Advisor: Qin Ding.
General note	Title from PDF t.p. (viewed February 21, 2014).
Dissertation note	M.S. East Carolina University 2013.
Bibliography note	Includes bibliographical references.
Technical details	System requirements: Adobe Reader.
Technical details	Mode of access: World Wide Web.

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AlienG2 : an automated analysis tool for genome-scale prediction of horizontal gene transfer / by Ali Ahmadvand.

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