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Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center
An improving method for estimating amino acid replacement modelsA Thesis Submitted for the degree ofMASTER OF COMPUTER SCIENCE IN THE FACULTY OF INFOR Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center RMATION TECHNOLOGYby LE VAN DATComputer ScienceInformation Technology, University of technology and engineering.National University. Hanoi. 144. Xuan Thuy, Hanoi. Viet Nam Hanoi 12, 2012Originality statement'I hereby declare that this submission is my own work and to the best of my knowledge it cont Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center ains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award ofTrung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center
any other degree or diploma at University of Engineering and Technology (UET/Coltech) or any other educational institution. except where due acknowledAn improving method for estimating amino acid replacement modelsA Thesis Submitted for the degree ofMASTER OF COMPUTER SCIENCE IN THE FACULTY OF INFOR Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center nowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.'Hanoi. 4,h December, 2012Si Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center gned: ...............AbstractAmino acid replacement models (amino acid substitution models or matrices) play important roles in protein phylogeneticsTrung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center
analysis and protein sequence alignment. Dayhofl was the first person who proposed a method to build amino acid models ill 1972. Currently, maximum liAn improving method for estimating amino acid replacement modelsA Thesis Submitted for the degree ofMASTER OF COMPUTER SCIENCE IN THE FACULTY OF INFOR Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center datasets, 'rhe most time consuming step in estimating matrices is buildingphylogenetics trees from protein alignments. In this thesis, we propose new methods to overcome the obstacle by splitting large alignments into small ones which still contain enough evolutionary information for estimating matr Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center ices.Experiments with both Pfam and FLU data sets show that proposed methods are about three to nine times faster than the best current method while tTrung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center
he quality of estimated matrices are nearly the same. Thus, our methods will enable researchers to estimate matrices from very large datasets.https://An improving method for estimating amino acid replacement modelsA Thesis Submitted for the degree ofMASTER OF COMPUTER SCIENCE IN THE FACULTY OF INFOR Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center Efficient Method for Estimating Amino Acid Substitution Models." KSE, pp.85-91, 2011. Third International Conference on Knowledge and Systems Engineering. 2011AcknowledgementsIwould like to thank my supervisor Lc Sy Vinh for fruitful discussions, excellent advises and friendly behavior.I want to th Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center ank Đr. Hoan Pham Tho for introducing me to Bioinforinatics and Dang Cao Cuong for supporting me a lot t hroughout my research.I express my gratitudeTrung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center
to my family and friends to help me and encourage me while doing this work.ContentsList of FiguresVList of TablesviGlossaryvii1Overview11.1Motivation.An improving method for estimating amino acid replacement modelsA Thesis Submitted for the degree ofMASTER OF COMPUTER SCIENCE IN THE FACULTY OF INFOR Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center cid sequences and amino acid substitutions...62.2Markov model....................................... 82.3Amino acid substitution models..................... 92.4Methods to estimate amino acid substitution models....102.4.1Counting methods............................ 10 Trung tâm Thư viện và Tri thức số - Library and Digital Knowledge Center An improving method for estimating amino acid replacement modelsA Thesis Submitted for the degree ofMASTER OF COMPUTER SCIENCE IN THE FACULTY OF INFORGọi ngay
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