Use a dynamic programming table to align TTGGATA and TGGATCATA using the local alignment method (Smith...
Use a dynamic programming table to align TTGGATA and TGGATCATA using the local alignment method (Smith and Waterman) with the following scoring scheme: gap: -5; mismatch: -3; match: +3.
Homework Answers
This refers to find the arrangement with the most positive value following such scheme. This means a match (same nucleotide in the same position) is the main thing to seek, if not posible then go to mismatchs (different nucleotides in the same position), and the least desired is a gap (a nucleotide and a gap in the same position). Biologically, this means substitutions are more facored than indel mutations. The alignment would be:
TTGGATA___
_TGGATCATA 5 matches (15), 1 mismatch (-3), and 0 gaps, a final value of 12
As we have 5 matches (15), 1 mismatch (-3), and 0 gaps, for a total value of 12. This was made naked eye, but now look at the result of a dynamic program as it is asked:
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Use a dynamic programming table to align TTGGATA and TGGATCATA
using the local alignment method (Smith...
Write the alignment matrix and the resulting best alignment of the following two sequences using the...
Write the alignment matrix and the resulting best alignment of the following two sequences using the scoring scheme: match = 2; mismatch = -1, gap penalty = -4 – gap length. The alignment matrix should have scores and trace-back arrows for every matrix element. Sequence1: TTCTCGAGACTCA Sequence2: TCTCGGACTCA
gatggggatac--tgtttggagcccaag gattggtacaccatattt---tactaag What is the score of the alignment using affine gap penalties with the following...
gatggggatac--tgtttggagcccaag gattggtacaccatattt---tactaag What is the score of the alignment using affine gap penalties with the following scoring parameters? match: +5 mismatch: -4 gap opening: -16 gap extension: -4 Note that these gap opening and gap extension scores are the same as the default parameters used by the EMBOSS matcher program. Please show the solutions
The Knapsack Problem in Python Not using the exhaustive search method or the Dynamic Programming ...
The Knapsack Problem in Python Not using the exhaustive search method or the Dynamic Programming Method, find another method that accomplishes the task of the knapsack problem in python. PLEASE DON'T USE THE EXHAUSTIVE SEARCH METHOD OR THE DYNAMIC PROGRAMMING METHOD, I DON'T NEED THOSE. THANK YOU.
Problem 1. (Calculating Edit Distance Using Dynamic Programming) A direct implementation of the above recursive scheme...
Problem 1. (Calculating Edit Distance Using Dynamic Programming) A direct implementation of the above recursive scheme will work, but it is spectacularly inefficient. If both input strings have N characters, then the number of recursive calls will exceed 2N. To overcome this performance bug, we use dynamic programming. Dynamic programming is a powerful algorithmic paradigm, first introduced by Bellman in the context of operations research, and then applied to the alignment of biological sequences by Needleman and Wunsch. Dynamic programming...
Align the same two sequences in part one with the new scoring scheme: This question relates...
Align the same two sequences in part one
with the new scoring scheme:
This question relates to
Bioinformatics --- Genome Sequence Analysis.
Below doesn't match the question above but should give you an
idea what it should look like. Answer should be in this format:
We would like to align two DNA sequences: (v) C GATACT, and (w) GATIC GT based on the following scoring scheme as discussed in class: i) s(i, j) = 1 if Vi = w; (matches);...
2. (12 marks) Use dynamic programming for the following 'Make Change problem': Number of denomina...
Can you answer #3?
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Using a while loop and \t output the following table (YOU CAN NOT USE ALL printf...
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Use the dynamic programming technique to find an optimal parenthesization of a matrix-chain product whose sequence...
Use the dynamic programming technique to find
an optimal parenthesization of a matrix-chain product whose
sequence of dimensions is <5, 8, 4, 10, 7, 50, 6>.
Matrix Dimension
A1 5*8
A2 8*4
A3 4*10
A4 10*7
A5 7*50
A6 50*6
You may do this either by implementing the MATRIX-CHAIN-ORDER
algorithm in the text or by simulating the algorithm by hand. In
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computation.
Using Floyd’s algorithm (See Dynamic Programming...
3) Solve the following Economic Dispatch problem using Dynamic Programming to find total minimum ...
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Problem 1. (Calculating Edit Distance Using Dynamic Programming) A direct implementation of the above recursive scheme will work, but it is spectacularly inefficient. If both input strings have N characters, then the number of recursive calls will exceed 2N. To overcome this performance bug, we use dynamic programming. Dynamic programming is a powerful algorithmic paradigm, first introduced by Bellman in the context of operations research, and then applied to the alignment of biological sequences by Needleman and Wunsch. Dynamic programming...
Align the same two sequences in part one
with the new scoring scheme:
This question relates to
Bioinformatics --- Genome Sequence Analysis.
Below doesn't match the question above but should give you an
idea what it should look like. Answer should be in this format:
We would like to align two DNA sequences: (v) C GATACT, and (w) GATIC GT based on the following scoring scheme as discussed in class: i) s(i, j) = 1 if Vi = w; (matches);...
Can you answer #3?
2. (12 marks) Use dynamic programming for the following 'Make Change problem': Number of denominations, N: 4 Denomination values, dl : 7, 2, 3,6 Amount for which change is to be made, A: 17. how the values of arrays Cl and SI (shown in class) for each denomination or iteration. 3. (8 marks) Implement Make Change problem' using dynamic programming and homw the outut fort he gdgg show the output for the input from Question 2....
Use the dynamic programming technique to find
an optimal parenthesization of a matrix-chain product whose
sequence of dimensions is <5, 8, 4, 10, 7, 50, 6>.
Matrix Dimension
A1 5*8
A2 8*4
A3 4*10
A4 10*7
A5 7*50
A6 50*6
You may do this either by implementing the MATRIX-CHAIN-ORDER
algorithm in the text or by simulating the algorithm by hand. In
either case, show the dynamic programming tables at the end of the
computation.
Using Floyd’s algorithm (See Dynamic Programming...
3) Solve the following Economic Dispatch problem using Dynamic Programming to find total minimum cost and P, P2, Ps, for load 300 MW? (25 points) 0 50 75 100 125 800 850 975 1000 1000 1250 1400 500 600 700
3) Solve the following Economic Dispatch problem using Dynamic Programming to find total minimum cost and P, P2, Ps, for load 300 MW? (25 points) 0 50 75 100 125 800 850 975 1000 1000 1250 1400 500 600 700
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