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The objective of the assignment is to program a pairwise alignment using the dynamic programming approach. Use the scoring scheme with the following base substitution scores and g for gap penalty (no affine gap penality). T C A T 20 10 5 5 C 10 20 5 5 А 5 5 5 20 10 G 5 5 10 20 The gap penalty is a variable, and use three different values of g, 5, 20, and 50 in order to determine the effect of the gap penalty. 1. Execute the dynamic programming on two datasets below, and for each set, determine that optimal alignments. You may have more than one alignment in each pair. a. AIGTIAT AICGTAG b. ATGAATGCGATTTCGGGTGGCC TTGGCAGGACATGAAGTTCGATACGGAA 2. Can you draw some conclusion on the impact of different values of gap penalty g? What to submit: You can use any programming language. Submit a report that includes the basic core of the dynamic programming routine, and aligned results of the test data set. The report should include a discussion on the result of the effect of the gap penalty. The source code in the appendix section. Namely, a source code itself is not a report.

The objective of the assignment is to program a pairwise alignment using the dynamic programming approach. Use the scoring scheme with the following base substitution scores and g for gap penalty (no affine gap penality). T C A T 20 10 5 5 C 10 20 5 5 А 5 5 5 20 10 G 5 5 10 20 The gap penalty is a variable, and use three different values of g, 5, 20, and 50 in order to determine the effect of the gap penalty. 1. Execute the dynamic programming on two datasets below, and for each set, determine that optimal alignments. You may have more than one alignment in each pair. a. AIGTIAT AICGTAG b. ATGAATGCGATTTCGGGTGGCC TTGGCAGGACATGAAGTTCGATACGGAA 2. Can you draw some conclusion on the impact of different values of gap penalty g? What to submit: You can use any programming language. Submit a report that includes the basic core of the dynamic programming routine, and aligned results of the test data set. The report should include a discussion on the result of the effect of the gap penalty. The source code in the appendix section. Namely, a source code itself is not a report.

Computer Networking: A Top-Down Approach (7th Edition)
Computer Networking: A Top-Down Approach (7th Edition)
7th Edition
ISBN:9780133594140
Author:James Kurose, Keith Ross
Publisher:James Kurose, Keith Ross
Chapter1: Computer Networks And The Internet
Section: Chapter Questions
Problem R1RQ: What is the difference between a host and an end system? List several different types of end...
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The objective of the assignment is to program a pairwise alignment using the dynamic programming approach. Use the scoring scheme with the following base substitution scores and g for gap penalty (no affine gap penality). T C T 20 10 5 С 10 20 5 А 5 A G 5 20 10 G 5 10 20 The gap penalty is a variable, and use three different values of g, 5, 20, and 50 in order to determine the effect of the gap penalty. 1. Execute the dynamic programming on two datasets below, and for each set, determine that optimal alignments. You may have more than one alignment in each pair. a. AIGTIAT AICGTAG b. ATGAATGCGATTTCGGGTGGCC TTGGCAGGACATGAAGTTCGATACGGAA 2. Can you draw some conclusion on the impact of different values of gap penalty g? What to submit: You can use any programming language. Submit a report that includes the basic core of the dynamic programming routine, and aligned results of the test data set. The report should include a discussion on the result of the effect of the gap penalty. The source code in the appendix section. Namely, a source code itself is not a report.
Transcribed Image Text:The objective of the assignment is to program a pairwise alignment using the dynamic programming approach. Use the scoring scheme with the following base substitution scores and g for gap penalty (no affine gap penality). T C T 20 10 5 С 10 20 5 А 5 A G 5 20 10 G 5 10 20 The gap penalty is a variable, and use three different values of g, 5, 20, and 50 in order to determine the effect of the gap penalty. 1. Execute the dynamic programming on two datasets below, and for each set, determine that optimal alignments. You may have more than one alignment in each pair. a. AIGTIAT AICGTAG b. ATGAATGCGATTTCGGGTGGCC TTGGCAGGACATGAAGTTCGATACGGAA 2. Can you draw some conclusion on the impact of different values of gap penalty g? What to submit: You can use any programming language. Submit a report that includes the basic core of the dynamic programming routine, and aligned results of the test data set. The report should include a discussion on the result of the effect of the gap penalty. The source code in the appendix section. Namely, a source code itself is not a report.
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