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.

View solution

Q. The program Profilemake can be used to produce a profile from an MSA.

View solution

Q. Which of the following is untrue regarding the block analysis method?

View solution

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

View solution

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.

View solution

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

View solution

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.

View solution

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

View solution

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

View solution

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

View solution

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

View solution

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

View solution

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.

View solution

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.

View solution

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

View solution

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

View solution

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

View solution

Q. Which of the following about MEME is untrue?

View solution

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

View solution

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

View solution