This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Comparative Genomics – 1”.
1. Comparative genomics includes a comparison of gene number, gene content, and gene location in both prokaryotic and eukaryotic groups of organisms.
Explanation: The availability of complete genome sequences makes possible a comparison of all of the proteins encoded by one genome, the proteome of that organism, with those of another. Because the genome sequence provides both the sequence and the map location of each gene, both the sequence and location can be compared.
2. Which of the following information Sequence comparisons do not provide?
a) Gene relationships
b) Function history
c) Evolutionary history
d) Gene locations
Explanation: Map locations of orthologous genes may also be compared. If a set of genes is grouped together at a particular chromosomal location, and if a set of similar genes is also grouped together in the genome of another organism, these groups share an evolutionary history.
3. Which of the given statements is incorrect?
a) Proteins may be clustered into families on the basis of either sequence or structural similarity
b) Proteins often comprise separate domains
c) The number of protein sequences that are available is insufficient to determine that domain shuffling occurs in evolution
d) Proteins are modular
Explanation: The number of protein sequences is sufficient unlike mentioned in option c. The comparisons of proteomes of different organisms can identify the type of domain changes and also provide an indication as to what biological role they may have in a particular organism.
4. Which of the given statements is incorrect?
a) Two tandem copies of a gene are produced while Proteins with new functions are produced
b) Proteins with new functions are produced by a gene duplication event
c) Assortment and reassortment of protein domains takes place in individual genomes
d) In no case the two duplicated genes both undergo change
Explanation: In a possibility, two duplicated genes both undergo change, but interactions between the proteins stabilize the original function and support the evolution of new ones. Through mutation and natural selection, one of the copies can develop a new function, leaving the other copy to cover for the original function. However, because most mutations are deleterious to function, often one of the copies becomes a pseudogene. Not all gene duplications are thought to have the above effects.
5. Which of the given statements is incorrect?
a) The processes of domain assortment and gene duplication produce families of proteins in organisms
b) Following speciation, a newly derived genome will inherit the families of ancestor organisms, but will also develop new ones to meet evolutionary challenges
c) Comparison of each of the proteins encoded by an organism with every protein, an all-against-all comparison, reveals which protein families have been amplified and what rearrangements have occurred as steps in the evolutionary process
d) When two or more proteins in the proteome share a high degree of similarity they are least likely to be paralogs
Explanation: When two or more proteins in the proteome share a high degree of similarity because they share the same set of domains, they are likely to be paralogs, genes that arose by gene duplication events. Proteins that align over shorter regions share some domains, but also may not share others. Although gene duplication events could have created such variation, other rearrangements may have also occurred, blurring the evolutionary history.
6. Which of the given statements is incorrect about All-against-all Self-comparison?
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
b) In all-against-all proteome comparison, each protein is used as a query in a similarity search against the remaining proteome
c) In all-against-all proteome comparison, the similar sequences are ranked by the quality and length of the alignments found
d) In all-against-all proteome comparison, The search is conducted with each alignment score receiving a statistical evaluation (P or E value)
Explanation: The domain content of these proteins may also be analyzed. in all-against-all proteome comparison, a match between a query sequence and another proteome sequence with the same domain structure will produce a high-scoring, highly significant alignment. These proteins are designated paralogs because they have almost certainly originated from a gene duplication event.
7. Which of the given statements is incorrect about Cluster analysis?
a) Clustering organizes the proteins into groups by some objective criterion
b) One criterion for a matching protein pair is the statistical significance of their alignment score
c) The P or E value from BLAST searches cannot be the criterion for a matching protein pair
d) A criterion for clustering proteins is the distance between each pair of sequences in a multiple sequence alignment
Explanation: Option c and b mean the same yet are different by the negation in option c.The lower this value, the better the alignment. There will be a cutoff P or E value at which the matches in the BLAST search are no longer considered significant. A value of P or E = 0.01–0.05 is usually the point at which the alignment score is no longer considered to be significant in order to focus on a more closely related group of proteins.
8. Which of the given statements is incorrect about Clustering by making subgraphs?
a) 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
b) One way to identify the most strongly supported clusters is simply to add the most weakly supported edges in the graph
c) One way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph
d) An edge is weighted according to the statistical significance of the alignment score
Explanation: As weaker and weaker links are removed, the remaining combinations of vertices and edges represent most strongly linked sequences. This type of analysis was performed on an initial collection of E. coli genes by Labedan and Riley (1995).
9. Which of the given statements is incorrect about Clustering by single linkage?
a) 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
b) A neighbor-joining algorithm is rarely used in this method
c) This procedure and the algorithms are the same as those used to make a phylogenetic tree by the distance methods
d) A distance matrix that shows the number of amino acid changes between each pair of sequences is made
Explanation: The matrix is then used to cluster the sequences by a neighbor-joining algorithm. These methods produce a tree or a different representation of the tree called a dendrogram, which minimizes the number of amino acid changes that would generate the group of sequences.
10. 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.
Explanation: In Hemophilus, 1247 of the total number of 1709 proteins do not have paralogs.
The core proteomes of the worm and fly are similar in size but with a greater number of duplicated genes in the worm. It is quite remarkable that the core proteome of the multicellular organisms (worm and fly) is only twice that of yeast.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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