Renyi Liu

Multiple sequence alignment plays a crucial role in extracting structural, functional, and evolutionary information from the exponentially growing sequence data from the ongoing genome sequencing. Based on the case study of retrotransposon sequence alignment, this thesis compares three alignment programs, DIALIGN, CLUSTALW, and PRRN, and proposes some strategies to improve alignment quality, such as realigning certain sequences or sequence ranges with different programs or parameters and hand editing. Entropy is used as an alignment quality indicator. This study also presents the design and development of an alignment tool, named AlignAgain, which is built to help biologists to improve alignment quality. AlignAgain is written in Java and allows users to display, edit, realign whole or partial sequences with CLUSTALW or PRRN, and append sequences with profile alignment. iv ACKNOWLEDGMENTS I would like to thank my major professor Dr. Eileen T. Kraemer for her patience in guiding me, encouraging me, and bearing with me throughout this study. This project can not be done without her invaluable advice on the design and implementation. My special thanks go to Dr. John Miller and Dr. Don Potter for being on my committee and for opening up new fields of knowledge to me through their classes. Eric Ganko for being an invaluable first user of this alignment tool. My greatest thanks go to my wife, my son, and my parents for their constant love and support.