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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Q. The GCG alignment programs have a RANDOMIZATION option, which shuffles the second sequence and calculates similarity scores between the unshuffled sequence and each of the shuffled copies.

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Q. Dayhoff, 1978- 1983, devised a second method for testing the relatedness of two protein sequences that can accommodate some local variation. Where this method is useful?

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Q. By whom and when were the Bayesian methods applied first?

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Q. With the application of Bayesian methods, the most probable repeat length and evolutionary time since the repeat was formed may be derived.

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Q. If the purpose is to calculate the probability of one event AND a second event, the odds scores for the events are _________

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Q. In a type of probability, analysis is to calculate the odds score for one event OR a second event, or of a series of events. In this case, the odds scores are _______

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Q. In Bayesian methods, difficulty with making estimations is that the estimate depends on the following Assumption.
(Assumption – The mutation rate in sequences has been constant with time and that the rate of mutation of all nucleotides is the same.)

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