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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Q. Which of the following is incorrect regarding PRRP?

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Q. In the program DIALIGN, pairs of sequences are aligned to locate aligned regions that do not include gaps, much like continuous diagonals in a dot matrix plot.

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Q. The Genetic Algorithm method has been recently adapted for MSA(Multiple Sequence Alignment) by Corpet (1998).

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Q. An approach for obtaining a higher-scoring MSA (Multiple Sequence Alignment) by rearranging an existing alignment uses a probability approach called simulated annealing.

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Q. The first step in Genetic Algorithm is arranging the sequences to be aligned in rows.

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Q. The second step in the Genetic Algorithm comprises of scoring of the 100 initial MSAs by the sum of pairs method.

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Q. In Genetic Algorithm, in the mutation process _______

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Q. The HMM is a statistical model that considers few combinations of matches and gaps to generate an alignment of a set of sequences.

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