Questions and answers for exam Preparation

MCQs

Total Questions : 165 | Page 4 of 17 pages

Question 31. Which of the given statements is incorrect about Clustering by single linkage?

In First step, a group of related sequences found in the all-against-all proteome comparison is subjected to a multiple sequence alignment usually by CLUSTALW
A neighbor-joining algorithm is rarely used in this method
This procedure and the algorithms are the same as those used to make a phylogenetic tree by the distance methods
A distance matrix that shows the number of amino acid changes between each pair of sequences is made

Discuss Question

Answer: Option B. -> A neighbor-joining algorithm is rarely used in this method
Answer: (b).A neighbor-joining algorithm is rarely used in this method

Question 32. Which of the given statements is incorrect about Clustering by making subgraphs?

Each sequence is a vertex and each pair of sequences that is matched with a significant alignment score is joined by an edge that is weighted according to the statistical significance of the alignment score
One way to identify the most strongly supported clusters is simply to add the most weakly supported edges in the graph
One way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph
An edge is weighted according to the statistical significance of the alignment score

Discuss Question

Answer: Option C. -> One way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph
Answer: (c).One way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph

Question 33. Which of the given statements is incorrect about All-against-all Self-comparison?

A comparison of each protein in the proteome with all other proteins distinguishes unique proteins from proteins that have arisen from gene duplication, and also reveals the number of protein families but the domain content of these proteins cannot be known
In all-against-all proteome comparison, each protein is used as a query in a similarity search against the remaining proteome
In all-against-all proteome comparison, the similar sequences are ranked by the quality and length of the alignments found
In all-against-all proteome comparison, The search is conducted with each alignment score receiving a statistical evaluation (P or E value)

Discuss Question

Answer: Option A. -> A comparison of each protein in the proteome with all other proteins distinguishes unique proteins from proteins that have arisen from gene duplication, and also reveals the number of protein families but the domain content of these proteins cannot be known
Answer: (a).A comparison of each protein in the proteome with all other proteins distinguishes unique proteins from proteins that have arisen from gene duplication, and also reveals the number of protein families but the domain content of these proteins cannot be known

Question 34. Which of the given statements is incorrect about Cluster analysis?

Clustering organizes the proteins into groups by some objective criterion
One criterion for a matching protein pair is the statistical significance of their alignment score
The P or E value from BLAST searches cannot be the criterion for a matching protein pair
A criterion for clustering proteins is the distance between each pair of sequences in a multiple sequence alignment

Discuss Question

Answer: Option C. -> The P or E value from BLAST searches cannot be the criterion for a matching protein pair
Answer: (c).The P or E value from BLAST searches cannot be the criterion for a matching protein pair

Question 35. The all-against-all analyses provide an indication as to the number of protein/gene families in an organism. This number represents the core proteome of the organism from which all biological functions have diversified.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option A. -> True
Answer: (a).True

Question 36. Which of the given statements is incorrect about Grouping Sequences?

The problem of deciding which sequences to include in the same group or cluster and which to separate into different groups or clusters is a recurring one
Divergence is necessary, but the sequences chosen should be clearly related based on inspection of each pair-wise alignment and a statistical analysis
The conservative approach is to group distinct sequences
The adventurous approach is to choose a set of marginally alignable sequences to pursue the difficult task of making a multiple sequence alignment and then to make profile models that may recognize divergence but will also give false predictions

Discuss Question

Answer: Option C. -> The conservative approach is to group distinct sequences
Answer: (c).The conservative approach is to group distinct sequences

Question 37. Which of the given statements is incorrect about the Comparison of proteomes to EST databases of an organism?

ESTs are single DNA sequence reads that contain a small fraction of incorrect base assessments, insertions, and deletions
Many sequences arise from near the 5’ end of the mRNA, although every effort is usually made to read as far 3’ as possible into the upstream portion of the cDNA
EST libraries are useful for preliminary identification of genes by database similarity searches
An EST database of an organism can be analyzed for the presence of gene families,
orthologs, and paralogs

Discuss Question

Answer: Option B. -> Many sequences arise from near the 5’ end of the mRNA, although every effort is usually made to read as far 3’ as possible into the upstream portion of the cDNA
Answer: (b).Many sequences arise from near the 5’ end of the mRNA, although every effort is usually made to read as far 3’ as possible into the upstream portion of the cDNA

Question 38. Which of the given statements is incorrect about Clusters of orthologous groups?

Using the protein from one of the organisms to search the proteome of the other for high-scoring matches should identify the ortholog as the highest- scoring match, or best hit
When entire proteomes of the two organisms are available, orthologs may be identified
a pair of orthologous genes in two organisms share so much sequence similarity that they may be assumed to have arisen from a common ancestor gene
each of the orthologs belongs to a family composed of paralogous sequences but irrelevant or not related to each other

Discuss Question

Answer: Option D. -> each of the orthologs belongs to a family composed of paralogous sequences but irrelevant or not related to each other
Answer: (d).each of the orthologs belongs to a family composed of paralogous sequences but irrelevant or not related to each other

Question 39. Which of the given statements is incorrect about Clusters of orthologous groups?

Paralogs may include a best hit or a high-scoring match of one of the sequences by another, but the reciprocal match can have low similarity that does not have to be significant
Paralogs defined by sets of three matching sequences in the selected organisms were kept separated from the clusters
Orthologous pairs were first defined by the best hits in reciprocal searches
To produce COGs, similarity searches were performed among the proteomes of phylogenetically distinct clades of prokaryotes

Discuss Question

Answer: Option B. -> Paralogs defined by sets of three matching sequences in the selected organisms were kept separated from the clusters
Answer: (b).Paralogs defined by sets of three matching sequences in the selected organisms were kept separated from the clusters

Question 40. Which of the given statements is incorrect about Searching for orthologs to a protein family in an EST database?

Searches of EST databases for matches to a query sequence routinely produce minimal amounts of output that must be searched manually for significant hits
ESTs with a high percent identity with the query sequence, a long alignment with the query sequence, and a very low E value of the alignment score represent groups of paralogous and orthologous genes
To identify orthologs as the most closely related sequence, ESTs were aligned using the amino acid alignment as a guide
To identify orthologs as the most closely related sequence, a phylogenetic tree was produced by the maximum likelihood method

Discuss Question

Answer: Option A. -> Searches of EST databases for matches to a query sequence routinely produce minimal amounts of output that must be searched manually for significant hits
Answer: (a).Searches of EST databases for matches to a query sequence routinely produce minimal amounts of output that must be searched manually for significant hits