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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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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