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

Title:	Algorithms and tools for splicing junction donor recognition in genomic DNA sequences
Author:	Yin, Maisheng
View Online:	njit-etd1997-112 (x, 83 pages ~ 2.1 MB pdf)
Department:	Department of Computer and Information Science
Degree:	Master of Science
Program:	Computer Science
Document Type:	Thesis
Advisory Committee:	Wang, Jason T. L. (Committee chair) McHugh, James A. (Committee member) Nassimi, David (Committee member)
Date:	1997-10
Keywords:	Genetic engineering. Nucleotide sequence--Computer programs. DNA.
Availability:	Unrestricted
Abstract:	The consensus sequences at splicing junctions in genomic DNA are required for pre-mRNA breaking and rejoining which must be carried out precisely. Programs currently available for identification or prediction of transcribed sequences from within genomic DNA are far from being powerful enough to elucidate genomic structure completely[4]. In this research, we develop a degenerate pattern match algorithm for 5' splicing site (Donor Site) recognition.. Using the Motif models we developed, we can mine out the degenerate pattern information from the consensus splicing junction sequences. Our experimental results show that, this algorithm can correctly recognize 93% of the total donor sites at the right positions in the test DNA group. And more than 91% of the donor sites the algorithm predicted are correct. These precision rates are higher than the best existing donor classification algorithm[25]. This research made a very important progress toward our full gene structure detection algorithm development.