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DYNAMIC PROGRAMMING to solve max cT u(cT) s.t. (�� <<11BF2B245F1C0740872D2843AD021A3E>]>> UMF011 – Introduction to bioinformatics, 2005 12 Dynamic programming Dynamic programming (DP) is an efficient recursive method to search through all possible alignments and finding the one with the optimal score. The method was developed by Richard Bellman in the 1950s and has found applications in numerous fields, from aerospace engineering to economics.. Computer science: theory, graphics, AI, systems, …. dynamic programming, Hidden Markov Model (HMM), Regression analysis, Artificial Neural Network (ANN), Clustering and Sequence Mining to analyse the given sequence. The framework of algebraic dynamic programming (ADP) allows us to express dynamic programming algorithms for sequence analysis on a high level of abstraction. (��ƏƊ8��(��)UK0UR���@ @�I��u7��I��o��T��#U��1� k�EzO��Yhr�y�켿_�x�G�a��k Bioinformatics. Viterbi algorithm) Bioinformatics (e.g. ���� JFIF �� C ! (�� shortest path algorithms) Graphical models (e.g. 0000041492 00000 n 0000004966 00000 n %&'()*456789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz��������������������������������������������������������������������������� (�� 5 0 obj The Dynamic-Programming Alignment Algorithm.It is quite helpful to recast the prob- lem of aligning twosequences as an equivalent problem of finding a maximum-score path in a certain graph, as has been observed by a number of authors, including Myers and Miller (1989). 0000001733 00000 n endstream m5�|�lڝ��9d�t���q � �ʼ. 7 0 R /Interpolate true /BitsPerComponent 8 /Filter /DCTDecode >> Dynamic programming in bioinformatics Dynamic programming is widely used in bioinformatics for the tasks such as sequence alignment, protein folding, RNA structure prediction and protein-DNA binding. Steps for Solving DP Problems 1. << /Type /Page /Parent 3 0 R /Resources 6 0 R /Contents 4 0 R /MediaBox [0 0 792 612] Define subproblems 2. Information theory.! In this paper, we exploit the analogy between protein sequence alignment and image pair correspondence to design a bioinformatics-inspired framework for stereo matching based on dynamic programming. Computer science: theory, graphics, AI, compilers, systems, É. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. Control theory. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. << /Length 12 0 R /Type /XObject /Subtype /Image /Width 437 /Height 500 /ColorSpace Dynamic programming is both a mathematical optimization method and a computer programming method. This document is highly rated by students and has been viewed 310 times. (�� Solution #2 – Dynamic programming • Create a big table, indexed by (i,j) – Fill it in from the beginning all the way till the end – You know that you’ll need every subpart – Guaranteed to explore entire search space • Ensures that there is no duplicated work – Only need to compute each sub-alignment once! 0000007949 00000 n The main idea of the Viterbi algorithm is to find the (�� endobj << /ProcSet [ /PDF /Text /ImageB /ImageC /ImageI ] /ColorSpace << /Cs1 7 0 R Computer science: theory, graphics, AI, compilers, systems, …. 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