Q. Alignment algorithms, both global and local, are fundamentally similar and only differ in the optimization strategy used in aligning similar residues.

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Q. In a dot matrix, two sequences to be compared are written in the _____________ of the matrix.

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Q. When the two sequences have substantial regions of similarity, many dots line up to form contiguous _______ lines.

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Q. A problem exists when comparing _____ sequences using the dot matrix method, namely, the _______

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Q. If the selected window size is too long, sensitivity of the alignment is lost.

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Q. A sequence can be aligned with itself to identify internal repeat elements.

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Q. Self complementarity of DNA sequences cannot be identified using a dot plot.

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Q. Which of the following is untrue about dot plot method and its applications?

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Q. The truly statistically significant sequence alignment will be able to provide evidence of homology between the sequences involved.

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Q. By calculating alignment scores of a large number of ______ sequence pairs, a distribution model of the ______ sequence scores can be derived.

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Q. Many studies have demonstrated that the distribution of similarity scores assumes a peculiar shape that resembles a highly skewed normal distribution with a long tail on one side. The distribution matches the _______

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Q. Which of the following is a part of the statistical test of sequences?

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Q. In the statistical test, randomization process in which one of the two given sequences is randomly shuffled.

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Q. What is used to generate parameters for the extreme distribution?

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Q. If the score is located in the extreme margin of the distribution, that means that the alignment between the two sequences is ______ due to random chance and is thus considered ______

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Q. It is not known whether the Gumble distribution applies equally well to gapped alignments.

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Q. Which of the following is untrue about the PRSS program?

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Q. The major disadvantage of the PRSS program is that it doesn’t allow partial shuffling.

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