The New Jersey Institute of Technology's
Electronic Theses & Dissertations Project

Title:	Fast program for sequence alignment using partition function posterior probabilities
Author:	Prasad, Meera
View Online:	njit-etd2011-081 (viii, 18 pages ~ 0.4 MB pdf)
Department:	Department of Computer Science
Degree:	Master of Science
Program:	Bioinformatics
Document Type:	Thesis
Advisory Committee:	Roshan, Usman W. (Committee chair) Wei, Zhi (Committee member) Wang, Jason T. L. (Committee member)
Date:	2011-05
Keywords:	Sequence alignment Probalign Partition function posterior probabilities
Availability:	Unrestricted
Abstract:	The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level. The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is also introduced.