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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Q. Which of the following is not true about iterative methods?

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Q. Which of the following is not among the methods for finding localized sequence similarity?

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Q. Profiles are found by performing the _____ MSA of a group of sequences and then removing the _______ regions in the alignment into a smaller MSA.

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Q. The program Profilemake can be used to produce a profile from an MSA.

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Q. Which of the following is untrue regarding the block analysis method?

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Q. Block analysis methods use substitution matrices such as the PAM and BLOSUM matrices to score matches.

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Q. In the method of extraction of blocks from a global or local MSA, a global MSA of related protein sequences usually includes regions that have been aligned without gaps in any of the sequences.

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Q. Which of the following is not true regarding the BLOCKS?

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