Bioinformatics Problem Set 8: Dynamic Programming and BLAST Exercises, Assignments of Chemistry

Download Bioinformatics Problem Set 8: Dynamic Programming and BLAST Exercises and more Assignments Chemistry in PDF only on Docsity! Page 1 of 3 CHEM 156 Winter 2002 Problem Set 8 Bioinformatics PRACTICE EXERCISES (Answers will be distributed the last day of class, and posted on VOH) 1. Apply the dynamic programming algorithm to fill in the alignment rectangle for the sequences ARSTV KTVIQ In each square of the alignment rectangle indicate the best move as a diagonal, vertical or horizontal. Use the scoring matrix given below, and for horizontal and vertical moves (gaps) apply a gap penalty of -5. A C D E F G H I K L M N P Q R S T V W Y A 5 -2 -1 -1 -2 0 -2 -1 0 -2 0 -1 -2 0 -1 1 0 0 -2 -1 C -2 15 -3 -1 -4 -3 -4 -4 -2 -2 -4 -1 -4 -3 -3 -3 -1 -2 -5 -5 D -1 -3 8 2 -3 -2 0 -3 -1 -2 -3 1 -1 -1 -1 -1 -1 -2 -3 -2 E -1 -1 2 6 -3 -2 -1 -3 1 -1 -2 -1 0 2 -1 0 -1 -2 -1 -1 F -2 -4 -3 -3 8 -3 -3 1 -1 2 0 -1 -4 -4 -1 -1 -1 1 1 3 G 0 -3 -2 -2 -3 7 -2 -3 -1 -3 -1 1 -2 -2 -2 1 -2 -3 -1 -2 H -2 -4 0 -1 -3 -2 12 -3 -2 -2 1 1 -1 -1 -1 -1 -2 -4 -4 0 I -1 -4 -3 -3 1 -3 -3 5 -2 2 1 -1 -1 -2 -3 -2 -1 4 -1 0 K 0 -2 -1 1 -1 -1 -2 -2 5 -2 0 0 0 0 2 0 0 -2 0 -1 L -2 -2 -2 -1 2 -3 -2 2 -2 5 3 -2 -3 -2 -2 -2 0 2 0 0 M 0 -4 -3 -2 0 -1 1 1 0 3 6 -1 -3 -1 0 -1 0 1 1 0 N -1 -1 1 -1 -1 1 1 -1 0 -2 -1 7 -2 1 -1 0 0 -2 -2 -2 P -2 -4 -1 0 -4 -2 -1 -1 0 -3 -3 -2 10 0 -2 -2 0 -3 -4 -3 Q 0 -3 -1 2 -4 -2 -1 -2 0 -2 -1 1 0 7 2 0 0 -3 -1 0 R -1 -3 -1 -1 -1 -2 -1 -3 2 -2 0 -1 -2 2 8 -1 -2 -1 0 0 S 1 -3 -1 0 -1 1 -1 -2 0 -2 -1 0 -2 0 -1 4 2 -1 -2 -1 T 0 -1 -1 -1 -1 -2 -2 -1 0 0 0 0 0 0 -2 2 5 1 -2 -2 V 0 -2 -2 -2 1 -3 -4 4 -2 2 1 -2 -3 -3 -1 -1 1 5 -2 0 W -2 -5 -3 -1 1 -1 -4 -1 0 0 1 -2 -4 -1 0 -2 -2 -2 16 3 Y -1 -5 -2 -1 3 -2 0 0 -1 0 0 -2 -3 0 0 -1 -2 0 3 8 V T S R A K T V I Q Page 2 of 3 Draw the resulting best alignment between the two sequences, by drawing lines between letters that should be aligned: ARSTV KTVIQ 2. Predict the most likely results of the BLAST and Dynamic Programming algorithms for the following sequence pairs. Do you expect the results to be the same for the two algorithms? Note : in the diagrams below, lines represent regions of no homology between the two sequences, solid regions represent regions of sequence similarity. A. B. BLAST DYNAMIC PROGRAMMING