Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) January 2010 Parallelization of dynamic programming recurrences in computational biology Arpith Jacob Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Jacob, Arpith, "Parallelization of dynamic programming recurrences in computational biology" (2010). All Theses and Dissertations (ETDs). 169. https://openscholarship.wustl.edu/etd/169 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact
[email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS School of Engineering and Applied Science Department of Computer Science and Engineering Thesis Examination Committee: Jeremy Buhler, Chair Michael Brent Ron Cytron Mark Franklin Robert Morley Bill Smart David Taylor PARALLELIZATION OF DYNAMIC PROGRAMMING RECURRENCES IN COMPUTATIONAL BIOLOGY by Arpith Chacko Jacob A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2010 Saint Louis, Missouri copyright by Arpith Chacko Jacob 2010 ABSTRACT OF THE THESIS Parallelization of dynamic programming recurrences in computational biology by Arpith Chacko Jacob Doctor of Philosophy in Computer Science Washington University in St. Louis, 2010 Research Advisor: Professor Jeremy Buhler The rapid growth of biosequence databases over the last decade has led to a per- formance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted.