Q. Dot plot of repeating elements would be small crosses on plot.

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Q. Use of the dynamic programming method requires a scoring system for the comparison of symbol pairs, and a scheme for GAP penalties.

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Q. After the derivation, the outputs of the dynamic programming are the ratios are called even scores.

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Q. The matrices PAM250 and BLOSUM62 contain _______

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Q. The higher is the score in the alignment _________

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Q. Gaps are added to the alignment because it ______

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Q. Which of the following is not a description of dynamic programming algorithm?

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Q. Which of the following is not a site on internet for alignment of sequence pairs?

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Q. Dayhoff PAM matrices, are based on an evolutionary model of protein change, whereas, BLOSUM matrices, are designed to identify members of the same family.

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Q. A feature of the dynamic programming algorithm is that the alignments obtained depend on the choice of a scoring system for comparing character pairs and penalty scores for gaps.

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Q. Which of the following is untrue regarding dynamic programming algorithm?

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Q. In scoring matrices, for convenience, odds scores are converted to log odds scores.

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Q. Which of the following doesn’t describe PAM matrices?

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Q. The assumption in this evolutionary model is that the amino acid substitutions observed over short periods of evolutionary history can be extrapolated to longer distances.

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Q. Which of the following is untrue about the modification of PAM matrices?

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Q. The Dayhoff model of protein evolution is not a Markov process.

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Q. Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?

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Q. The more conserved amino acids in similar proteins from different species are ones that play an essential role in structure and function and the less conserved are in sites that can vary without having a significant effect on function.

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Q. A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______

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Q. In the GCG and FASTA program suites, the scoring matrix itself is formatted in a way that includes default ______

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