Statistical Methods for Aiding Alignment MCQ

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• Which of the following about the Gibbs sampler is untrue?
  ক

  It is a statistical method for finding motifs in sequences

  খ

  It is dissimilar to the principle of the EM method

  গ

  It searches for the statistically most probable motifs

  ঘ

  It can find the optimal width and number of given motifs in each sequence
• Which of the following about MEME is untrue?
  ক

  It is a Web resource for performing local MSAs (Multiple Sequence Alignment) by the above expectation maximization method is the program MEME

  খ

  It stands for Multiple EM for Motif Elicitation

  গ

  It was developed at developed at the University of California at San Diego Supercomputing Center

  ঘ

  The Web page has multiple versions for searching blocks by an EM algorithm
• An alternative method is to produce an odds scoring matrix calculated by dividing each base frequency by the background frequency of that base.
  ক

  True

  খ

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

  True

  খ

  False
• 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.
  ক

  True

  খ

  False
• 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.
  ক

  30

  খ

  10

  গ

  25

  ঘ

  20
• Out of the two repeated steps in EM algorithm, the step 2 is ________
  ক

  the maximization step

  খ

  the minimization step

  গ

  the optimization step

  ঘ

  the normalization step
• Which of the following is untrue regarding Expectation Maximization algorithm?
  ক

  An initial guess is made as to the location and size of the site of interest in each of the sequences, and these parts of the sequence are aligned

  খ

  The alignment provides an estimate of the base or amino acid composition of each column in the site

  গ

  The column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences

  ঘ

  The row-by-column composition of the site already available is used to estimate the probability
• The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only.
  ক

  True

  খ

  False