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Repclass Theses

Repclass Theses

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Published by: rnirmal on Dec 24, 2008
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REPCLASS: CLUSTER AND GRID ENABLED AUTOMATIC CLASSIFICATIONOF TRANSPOSABLE ELEMENTS IDENTIFIED DE NOVO INGENOME SEQUENCESbyNIRMAL RANGANATHANPresented to the Faculty of the Graduate School of The University of Texas at Arlington in Partial Fulfillmentof the Requirementsfor the Degree of MASTER OF SCIENCE IN COMPUTER SCIENCE AND ENGINEERINGTHE UNIVERSITY OF TEXAS AT ARLINGTONDecember 2005
 
ACKNOWLEDGEMENTSI would like to thank my supervising professor, Mr. David Levine, Departmentof Computer Science and Engineering for his constant encouragement and support,providing me guidelines in my research work.I would like to thank Dr. Cedric Feschotte, Department of Biology for havingprovided constant encouragement and direction in my thesis work and for having agreat deal of patience in explaining the intricacies of the Biology involved.I would like to thank Dr. Nikola Stojanovic, Department of Computer Scienceand Engineering for serving on my committee.I would like to thank Patrick Mcguigan for helping out in troubleshooting issueson the cluster and providing all the extra resources I needed.I would like to thank my friends who provided constant support and helped mewith my other obligations.Finally, my sincerest gratitude to Mum and Dad who have always been there forme, providing constant encouragement and support.November 11, 2005ii
 
ABSTRACTREPCLASS: CLUSTER AND GRID ENABLED AUTOMATIC CLASSIFICATIONOF TRANSPOSABLE ELEMENTS IDENTIFIED DE NOVO INGENOME SEQUENCESPublication No. ______Nirmal Ranganathan, M.S.The University of Texas at Arlington, 2005Supervising Professor: David LevineIn the last few years many computer and laboratory improvements in theproduction and analysis of DNA sequences have made possible the completesequencing of whole genomes. This provides us with a wealth of raw genomes thatneeds to be processed and annotated. 5% to 80% of eukaryotic genomes containrepetitive DNA consisting of transposable elements and tandem repeats which needs tobe identified, classified and annotated in order to sequence and annotate the entiregenome accurately.Existing tools allow us to identify and annotate transposable elements (TE) butno tool exists for their classification. This thesis work introduces REPCLASS aniii

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