Q. A dotplot is a visual and qualitative technique whereas the sequence alignment is an exact and quantitative measure of similarity of alignments.

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Q. The global sequence alignment is suitable when the two sequences are of dissimilar length, with a negligible degree of similarity throughout.

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Q. The alignment score is the sum of substitution scores and gap penalties in this type of algorithm.

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Q. The substitution matrices are rarely used in this type of matching.

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Q. Which of the following is untrue about Protein substitution matrices?

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Q. In Needleman-Wunsch algorithm, the gaps are scored -2.

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Q. The number of possible global alignments between two sequences of length N is _____

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Q. Which of the following is untrue about Needleman-Wunsch algorithm?

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Q. There are two types matrices involved in the study- score matrices and trace matrices.

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Q. Progressive alignment methods use the dynamic programming method to build an MSA starting with the most related sequences and then progressively adding less related sequences or groups of sequences to the initial alignment.

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Q. Progenitor sequences represented by the ______ branches of the tree are derived by alignment of the _______ sequences.

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Q. CLUSTALW is a more recent version of CLUSTAL with the W standing for ________

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Q. The CLUSTALX provides a graphic interface.

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

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Q. The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?

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Q. The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment.

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Q. Like other alignment programs, CLUSTAL uses a null score for opening a gap in a sequence alignment and a penalty for extending the gap by one residue.

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

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Q. The resulting tree is then used to guide the alignment of the most closely related sequences and groups of sequences. The resulting alignment is a global alignment produced by the Needleman-Wunsch algorithm.

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Q. Iterative methods include repeatedly realigning subgroups of the sequences and then by aligning these subgroups into a local alignment of all of the sequences.

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