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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Q. The pattern searching method type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.

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Q. Although MOTIF program is used successfully for making the BLOCKS database, it is limited in the pattern sizes that can be found.

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

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Q. The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only.

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Q. Which of the following is untrue regarding Expectation Maximization algorithm?

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Q. Out of the two repeated steps in EM algorithm, the step 2 is ________

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Q. In EM algorithm, as an example, suppose that there are 10 DNA sequences having very little similarity with each other, each about 100 nucleotides long and thought to contain a binding site near the middle 20 residues, based on biochemical and genetic evidence. The following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the ______ sequences.

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