Q. If a good sampling of sequences is _______ the number of sequences is _________ and the motif structure is ________ it should, in principle, be possible to obtain frequencies highly representative of the same motif in other sequences also.

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Q. Two considerations arise in trying to tune the PSSM so that it adequately represents the training sequences. Which of the following is not their description?

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Q. The quality and quantity of information provided by the PSSM also varies for ________ in the motif.

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Q. Analysis of MSAs for conserved blocks of sequence leads to production of the position-specific scoring matrix.

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Q. Which of the following about the Gibbs sampler is untrue?

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Q. Which of the following about MEME is untrue?

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Q. An alternative method is to produce an odds scoring matrix calculated by dividing each base frequency by the background frequency of that base.

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Q. For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.

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Q. In the intermediate steps of EM algorithm, the number of each base in each column is determined and then converted to fractions.

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Q. In the initial step of EM algorithm, the 20-residue-long binding motif patterns in each sequence are aligned as an initial guess of the motif.

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

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

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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 not true regarding the BLOCKS?

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

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

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