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

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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. Which of the following about MEME is untrue?

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

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

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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. 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. If the data set is _______ then unless the motif has __________ amino acids in each column, the column frequencies in the motif may not be highly representative of all other occurrences of the motif.

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Q. Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.

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Q. Which of the following is not a feature of editors and formatters?

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Q. GDE (Genetic Data Environment) provides a general interface on UNIX machines for sequence analysis, sequence alignment editing, and display.

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Q. MACAW is a local multiple sequence alignment program only.

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Q. Two commonly encountered examples are the Genetics Computer Group’s MSF format and the CLUSTALW ALN format.

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