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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Q. In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.

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Q. On analysis of the alignment scores of random sequences will reveal that the scores follow a different distribution than the normal distribution called the _________

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Q. The statistical analysis of alignment scores is much better understood for ________ than for _______

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Q. When random or unrelated sequences are compared using a global alignment method, they can have ____________ reflecting the tendency of the global algorithm to match as many characters as possible.

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Q. Which of the following are not related to Needleman-Wunsch alignment algorithm?

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Q. Waterman, in1989, provided a set of means and standard deviations of global alignment scores between random DNA sequences, using mismatch and gap penalties that produce a linear increase in score with _______ a distinguishing feature of global alignments.

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Q. Who suggested that the global alignment scores between unrelated protein sequences followed the extreme value distribution, similar to local alignment scores? And when?

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Q. _______ analyzed the distribution of scores among 100 vertebrate nucleic acid sequences and compared these scores with randomized sequences prepared in different ways.

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Q. If the random sequences were prepared in a way that maintained the local base composition by producing them from overlapping fragments of sequence, the distribution of scores has a _______ standard deviation that is closer to the distribution of the natural sequences.

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