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Unformatted text preview: Computational Biology, Part 3 Sequence Comparison with Dynamic Programming and Similarity Matrices Robert F. Murphy Copyright © 1996, 1999-2006. Copyright All rights reserved. Dynamic programming algorithms for sequence comparison s Builds on concept of dot matrix s Introduced for biological sequences by x S. B. Needleman & C. D. Wunsch. A general S. method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453 (1970) Mol. Steps of basic dynamic programming alignment method s 1. Initialize matrix to match scores (0 or 1) s 2. Do summation operation x Finds the maximum number of matches that can Finds be obtained starting at any position and proceeding "forward" proceeding s 3. Traceback to find maximum match 3. alignment alignment Summation operation 1. Start in lower right corner 2. Move up one position and left one position 3. Find largest value in either (a) row segment 3. starting one below current position and extending to the right or (b) column segment starting one to the right of current position and extending down position Summation operation (cont.) 4. Add this value to the value in the current 4. cell cell 5. Repeat steps 3 and 4 for all cells to the left 5. in current row and all cells above in current column column 6. If we are not in the top left corner, go to 6. step 2 step ----V HGQKV ----VA HGQKVA ----VADALTK HGQKVADALTK ----VADALTK HGQKVADALTK ----VADALTKPVNFKFA HGQKVADALTK------A ----VADALTKPVNFKFAVAH HGQKVADALTK------AVAH Illustration of Simple Dynamic Programming Method s (Demonstration A8) Use of dynamic programming to evaluate homology between pairs of sequences s If we just want to know maximum match If possible between two sequences, don't need to do traceback but can just look at the highest value in the first row or column ("match score&...
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This note was uploaded on 01/13/2012 for the course BIO 101 taught by Professor Staff during the Fall '10 term at DePaul.

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