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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Q. If the two sequences share significant similarity, it is extremely ______ that the extensive similarity between the two sequences has been acquired randomly, meaning that the two sequences must have derived from a common evolutionary origin.

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Q. Sometimes, it is also possible that two sequences have derived from a common ancestor, but may have diverged to such an extent that the common ancestral relationships are not recognizable at the sequence level.

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Q. Which of the following is incorrect regarding sequence homology?

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Q. Sequence similarity can be quantified using ________ homology is a ______ statement.

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Q. Shorter sequences require higher cutoffs for inferring homologous relationships than longer sequences.

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Q. Sequence similarity and sequence identity are synonymous for nucleotide sequences and protein sequences as well.

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Q. The overall goal of pair wise sequence alignment is to find the best pairing of two sequences, such that there is maximum correspondence among residues.

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Q. In local alignment, the two sequences to be aligned cannot be of unequal lengths.

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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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