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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Q. Another difficulty in Bayesian methods is deciding on the length of sequence that was duplicated.

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Q. A length and distance that gives the highest overall probability may then be determined. Such alignments are initially found using ________

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Q. Which of the following feature of Bayesian methods is the disadvantage of it?

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Q. Zhu (1998) have devised a computer program called the Bayes block aligner which in effect slides ____ sequences along each other to find the ______ ungapped regions or blocks.

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Q. Unlike the commonly used methods for aligning a pair of sequences, the Bayesian method _______ using a particular scoring matrix or designated gap penalties.

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Q. Which of the following is incorrect regarding pair wise sequence alignment?

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Q. Which of the following is incorrect about evolution?

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Q. The presence of evolutionary traces is because some of the residues that perform key functional and structural roles tend to be preserved by natural selection; other residues that may be less crucial for structure and function tend to mutate more frequently.

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Q. The degree of sequence variation in the alignment reveals evolutionary relatedness of different sequences, whereas the conservation between sequences reflects the changes that have occurred during evolution in the form of substitutions, insertions, and deletions.

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