Bioinformatics Mcqs

Page No. 63

Neighbor-joining chooses the sequences that should be joined to give the best least squares estimates of the branch lengths that most closely reflect the actual distances between the sequences.


a True

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b False

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ceither true and false

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dnone of these

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View Answer True

Which of the following is untrue regarding the neighbor-joining method?


aIt is very much like the Fitch-Margoliash method

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b It is totally dissimilar than the Fitch-Margoliash method

✓


cIt is especially suitable when the rate of evolution of the separate lineages under consideration varies

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d When the branch lengths of trees of known topology are allowed to vary in a manner that simulates varying levels of evolutionary change, it is the most reliable method

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View Answer It is totally dissimilar than the Fitch-Margoliash method

Which of the following is untrue regarding the Distance analysis programs in PHYLIP?


a FITCH estimates a phylogenetic tree assuming additivity of branch lengths

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bFITCH uses the Fitch-Margoliash method

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cFITCH assumes a molecular clock but KITSCH does no

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dNEIGHBOR estimates phylogenies using the neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA)

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View Answer FITCH assumes a molecular clock but KITSCH does no

Which of the following is untrue regarding the distance methods?


aThe sequence pairs that have the largest number of sequence changes between them are termed ‘neighbors’

✓


bOn a tree, these sequences share a node or common ancestor position and are each joined to that node by a branch

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cIt produces a phylogenetic tree of the group

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dIt employs the number of changes between each pair in a group of sequences

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View Answer The sequence pairs that have the largest number of sequence changes between them are termed ‘neighbors’

Parsimony can give ________ information when rates of sequence change _______ in the different branches of a tree that are represented by the sequence data.


amisleading, vary

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b useful, change

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cmisleading, are constant

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d sometimes contradicting, are constant

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View Answer misleading, vary

PROTPARS counts the minimum number of mutations to change a codon for the first amino acid into a codon for the second amino acid, but only scores those mutations in the mutational path that actually change the amino acid


a True

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b False

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ceither true and false

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dnone of these

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View Answer True

Which of the following is untrue regarding the programs for analysis of nucleic acid sequences?


aDNAPARS treats gaps as a fifth nucleotide state

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bDNAPENNY performs parsimonious phylogenies by branch-and-bound search

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cDNAPENNY can analyze sequences up to 11 or 12

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dCompatibility criterion is not involved in DNACOMP

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View Answer Compatibility criterion is not involved in DNACOMP

Which of the following is untrue regarding the maximum parsimony method?


aThis method predicts the evolutionary tree

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b It minimizes the number of steps required to generate the observed variation in the sequences

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cThe method is also sometimes referred to as the minimum evolution method

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dOnly a pairwise sequence alignment is required to predict which sequence positions are likely to correspond

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View Answer Only a pairwise sequence alignment is required to predict which sequence positions are likely to correspond

A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?


aThe basis of this method is to devise a scheme for introducing substitutions, insertions, and gaps into sequences

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b The basis of this method is to provide a probability that each of these changes occurs over certain periods of evolutionary time

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cGiven each of these predicted changes, the method examines all the possible combinations of mutations to change one sequence into another

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dMultiple combinations are selected that will be the most likely over time

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View Answer Multiple combinations are selected that will be the most likely over time

Once all positions in the sequence alignment have been examined, the likelihoods given by each column in the alignment for each tree are _____ to give the likelihood of the tree.


amultiplied

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badded

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c divided

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d squared

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View Answer multiplied

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