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miami1273245641.pdf (1.02 MB)
ETD Abstract Container
Abstract Header
MST Based
Ab Initio
Assembler of Expressed Sequence Tags
Author Info
Zhang, Yuan
Permalink:
http://rave.ohiolink.edu/etdc/view?acc_num=miami1273245641
Abstract Details
Year and Degree
2010, Master of Computer Science, Miami University, Computer Science and Systems Analysis.
Abstract
In the thesis we present a new algorithm for the assembly of ESTs based on a minimum spanning tree construction. By representing the EST input as a graph, quickly assigning edge weights with a new distance heuristic for detecting edge overlap, and calculating a minimum spanning tree, we find that we can use a quick transversal of this tree to accurately order the EST set, filter out extraneous ESTs, correct errors and infer the actual transcript sequence from which the set was generated. Implementing this into a software tool, we find that our tool gives us results better than CAP3, the leading EST assembly tool in the literature. In this paper we will explain the EST assembly problem, outline the assembly algorithm, and present a quantitative comparison against the results of CAP3.
Committee
John Karro, PhD (Advisor)
Mufit Ozden, PhD (Committee Member)
Chun Liang, PhD (Committee Member)
Pages
48 p.
Subject Headings
Bioinformatics
Keywords
EST assembly
;
assembler
;
minimum spanning tree
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Citations
Zhang, Y. (2010).
MST Based
Ab Initio
Assembler of Expressed Sequence Tags
[Master's thesis, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami1273245641
APA Style (7th edition)
Zhang, Yuan.
MST Based
Ab Initio
Assembler of Expressed Sequence Tags.
2010. Miami University, Master's thesis.
OhioLINK Electronic Theses and Dissertations Center
, http://rave.ohiolink.edu/etdc/view?acc_num=miami1273245641.
MLA Style (8th edition)
Zhang, Yuan. "MST Based
Ab Initio
Assembler of Expressed Sequence Tags." Master's thesis, Miami University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=miami1273245641
Chicago Manual of Style (17th edition)
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Document number:
miami1273245641
Download Count:
377
Copyright Info
© 2010, all rights reserved.
This open access ETD is published by Miami University and OhioLINK.