NJIT eTD::njit-etd2011-081::Prasad, Meera::"Fast program for sequence alignment using partition function posterior probabilities"

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.

Title:	Fast program for sequence alignment using partition function posterior probabilities
Author:	Prasad, Meera
Document Type:	Thesis
Department:	Department of Computer Science
Degree:	Master of Science
Major:	Bioinformatics
Advisory Committee:	Roshan, Usman W. Wei, Zhi Wang, Jason T. L.
Thesis Date:	2011, May
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.
Complete Thesis:	njit-etd2011-081 (28 pages ~ 396 KB pdf)
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