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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