Which of the given statement is incorrect regarding MAGPIE?

It automatically annotates genomic sequence data and maintains a daily up-to-date record in response to user queries about one or more genomes

It analyzes the genome using a set of automated processes

It is designed for high-throughput genome sequence analysis

It is unable to locate potential promoters

It automatically annotates genomic sequence data and maintains a daily up-to-date record in response to user queries about one or more genomes

Which of the given statements is incorrect about Horizontal Gene Transfer?

It is a significant source of genome variation in bacteria, allowing them to exploit new environments

Such transfer is rendered possible by a variety of natural mechanisms in bacteria for transferring DNA from one species to another

Detection of HT is made possible by the fact that each genome of each bacterial species has a unique base composition

The time of transfer of DNA cannot be estimated by the composition of the HT DNA

Genes that are transcribed are located in the ______

heterochromatin and euchromatin

Which of the following information is not directly obtained by microarray analysis?

Genes that respond to a given environmental signal to the same extent

Which genes are expressed at a particular stage of the cell cycle

Which genes are expressed at a particular stage of developmental cycle of an organism

Which genes are depleted at what time

Genes that respond to a given environmental signal to the same extent

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

An edge is weighted according to the statistical significance of the alignment score

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

In case of genome sequence assembly which of the given statement is incorrect?

Genome sequences are assembled from DNA sequence fragments of approximate length 500 bp obtained using DNA sequencing machines

Full chromosomal sequences are assembled from the overlaps in a highly redundant set of fragments by an automatic computational method or from the fragment order on a physical map

Chromosome cloning is carried out in bacterial artifical chromosomes (BACs)

Chromosomes of a target organism are purified, fragmented, and subcloned in fragments of size hundreds of bp

Genome sequences are assembled from DNA sequence fragments of approximate length 500 bp obtained using DNA sequencing machines

Which of the given statements is incorrect about Ancient Conserved Regions?

These ACRs may represent proteins present at the time of the prokaryotic–eukaryotic divergence

The method involves database similarity searches of the SwissProt database with human, worm, yeast, or E. coli genes and identification of matches with sequences from a different phylum than the query sequence

An analysis of ACRs that predate the radiation of the major animal phyla some 580–540 million years ago suggested that 50–60% of coding sequences are ACRs

These ACRs may represent proteins present at the time of the prokaryotic–eukaryotic divergence

Phylogenetically diverse groups of organisms have been analyzed for the presence of conserved proteins and protein domains that have been conserved over long periods of evolutionary time, called ancient conserved regions or ACRs

Evolutionary modeling can include various types of analyses. Which is mostly not one of them?

Duplications at gene, chromosomal and full genome level

The prediction of chromosomal rearrangements

Duplications at gene, chromosomal and full genome level

Duplications at the protein domain level

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

EST libraries are useful for preliminary identification of genes by database similarity searches

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

In cluster analysis of microarray data– If Xi is the log odds value for gene X at time i, then for two genes X and Y and N observations, a similarity score is calculated. S(X,Y) is also known as the Pearson correlation coefficent. Xoffset and Yoffset can be the mean of the observations on X or Y, respectively, in which case is the standard deviation, or else Xoffset and Yoffset can be set to zero when a reference state is used. Which of the following best represents it?

S(X,Y) = \(\frac{1}{N-1}\) ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY

S(X,Y) = \(\frac{1}{N-2}\) ∑i=1,N . (Xi – Xoffset) (Yi + Yoffset)/ϕxQY

S(X,Y) = \(\frac{1}{N}\) ∑i=1,N . (Xi – Xoffset) (Yi – Yoffset)/ϕxQY

S(X,Y) = \(\frac{1}{N-1}\) ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY

S(X,Y) = \(\frac{1}{N}\) ∑i=1,N+2 . (Xi + Xoffset) (Yi – Yoffset)/ϕxQY

______ can comprise a large proportion of the eukaryotic genome as ______

macrosatellite DNA elements, single copy sequences

transposable elements, single copy sequences

transposable elements, repetitive sequences

macrosatellite DNA elements, single copy sequences

satellite DNA elements, single copy sequences

The designation ECa.b.c.d conveys information. Which of the following is not one of it?

The group of substrate molecule

One of twelve main classes of biochemical reactions

The group of substrate molecule

The nature of chemical bond that is involved in the reaction

Designation for acceptor molecules (cofactors)

Which of the given statement is incorrect about the gene map?

Sequence variations (polymorphisms) that are close to (tightly linked) a trait may be used to trace the trait by virtue of the fact that the polymorphism and the trait are seldom separated from one generation to the next

Gene order in two related organisms reflects the order that was present in a common ancestor genome. Chromosomal breaks followed by reassembly of fragments in a different order can produce new gene maps

Gene order is only revealed by the physical order of genes on the chromosome

Sequence variations (polymorphisms) that are close to (tightly linked) a trait may be used to trace the trait by virtue of the fact that the polymorphism and the trait are seldom separated from one generation to the next

These types of evolutionary changes in genomes have been modeled by computational methods

Which of the given statement is incorrect about Clusters of functionally related genes?

As the relationship between the organisms decreases, local groups of genes remain clustered together, but chromosomal rearrangements move the clusters to other locations

In microbial genomes, genes specifying a metabolic pathway may be contiguous on the genome where they are coregulated transcriptionally in an operon by a common promoter

In related organisms, gene order on the chromosome is least likely to be conserved

As the relationship between the organisms decreases, local groups of genes remain clustered together, but chromosomal rearrangements move the clusters to other locations

The function of a particular gene can sometimes be predicted, given the known function of a neighboring, closely linked gene

In Protein 2D gel Electrophoresis, Individual proteins produced by the genome can be separated to _____ by this method and specific ones identified by various _______

a large extent, biochemical tests only

smaller extent, biochemical and immunological tests

a large extent, biochemical and immunological tests

a large extent, biochemical tests only

smaller extent, purely mechanical tests

Which of the given statement is incorrect about Orthologs?

The best hit in each proteome is likely to be with an ortholog of the query gene

In comparing two proteomes, a common standard is to require that for each pair of orthologs, the first of the pair is the best hit when the second is used to query the proteome of the first

To identify orthologs, each protein in the proteome of an organism is used as a query in a similarity search of a database comprising the proteomes of only one different organism

The best hit in each proteome is likely to be with an ortholog of the query gene

Orthologs are genes that are so highly conserved by sequence in different genomes that the proteins they encode are strongly predicted to have the same structure and function and to have arisen from a common ancestor through speciation

Which of the given statements is incorrect about Microarray Analysis?

The proteins are first separated in a column on the basis of size and then across a second dimension on a slab on the basis of charge

It is designed to detect global changes in transcription in a genome

It provides information about the levels of protein products of the genes

The proteins are first separated in a column on the basis of size and then across a second dimension on a slab on the basis of charge

Labeled protein samples may also be extracted from treated cells and separated by two-dimensional gel electrophoresis

Other types of evidence for a relationship between two genes are also given that are not dependent in sequence similarity. Which of the following is a wrong statement?

genes are closely linked on the same chromosomes

genes are transcribed from the same DNA strand

gene fusions are observed between otherwise separate genes

phylogenetic profiles show the genes are not that commonly present in organisms

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

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

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

156 + Mcqs in Dna Genomic Sequencing in Bioinformatics Page 1 McqOptions

1.	Which of the given statement is incorrect regarding MAGPIE?
A.	It analyzes the genome using a set of automated processes
B.	It is designed for high-throughput genome sequence analysis
C.	It is unable to locate potential promoters
D.	It automatically annotates genomic sequence data and maintains a daily up-to-date record in response to user queries about one or more genomes
Answer» D. It automatically annotates genomic sequence data and maintains a daily up-to-date record in response to user queries about one or more genomes

2.	While sequencing of The first bacterial genome—Approximately ____ of the ____ predicted genes matched genes of another species, the bacterial species E. coli K-12 that had been the subject of many years of genetic and biochemical research.
A.	46%, 1500
B.	58%, 1496
C.	72%, 1743
D.	58%, 1743
Answer» E.

4.	Vertebrate chromosomes have long (>300 kb) regions of distinct GC richness, repeat content, and gene density, designated isochores in a model of genome organization proposing that genomes are made up of distinct segments of unique composition.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

5.	The hierarchical clustering method generates a similarity score [S(X,Y)] for all gene combinations, places the scores in a matrix, joins those genes that have the highest score, and then continues to join progressively less similar pairs.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

6.	The results of searches in separate fields may be combined to narrow down the choices.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

7.	When two proteins share a considerable degree of sequence identity throughout the sequence alignment, they are least likely to share the same function.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

8.	Sequencing of genomes depends on the assembly of a large number of DNA reads into a linear, contiguous DNA sequence.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

9.	The program returns the number of matches found and provides an opportunity to narrow this list by including more terms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

10.	Genes that are transcribed are located in the ______
A.	euchromatin
B.	heterochromatin
C.	heterochromatin and euchromatin
D.	tightly bound DNA
Answer» B. heterochromatin

11.	In protein/domain analysis, each protein in the predicted proteome is again used as a query of a curated protein sequence database such as ____ in order to locate similar domains and sequences. To find orthologs, very low E value scores (E<10<20) for the alignment score and an alignment that includes 60–80% of the query sequence are generally required in order to avoid matches to paralogs.
A.	PubChem
B.	Genbank
C.	MeSH
D.	SwissProt
Answer» E.

12.	In examining the results of analysis, it is important to look for the method used the statistical significance of the result, and the overall degree of confidence in the alignments.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

21.	In cluster analysis of microarray data– For n genes, the process is repeated ________ times until a single element remains.
A.	n²
B.	n
C.	n¯¹
D.	n¯⁴
Answer» D. n¯⁴

24.	Yeast is about ______ compact than E. coli.
A.	fivefold, less
B.	threefold, more
C.	twofold, less
D.	twofold, more
Answer» D. twofold, more

26.	_______ of the Drosophila sequence is composed of TEs and _____ is heterochromatic regions that do not include genes.
A.	one-fourth, one-third
B.	one-fifth, one-fourth
C.	one-sixth, one-eighth
D.	one-sixth, one-third
Answer» E.

32.	WU-BLAST produces P scores and BLAST (NCBI) produces E scores where _________
A.	E = ln (1 + P²)
B.	E = ln (1 – P²)
C.	E = ln (1 + P)
D.	E = ln (1 – P)
Answer» E.

13.	The sequences of satellite DNA fall into different types, each with a different repeat unit of length _____
A.	5–400 Mbp
B.	3–300 kbp
C.	6–900 Mbp
D.	5–200 bp
Answer» E.

16.	In the program COGNITOR each protein in the proteome is used as a query of a database of protein clusters.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

18.	Each genome sequence is scanned for protein-encoding genes using gene models trained on known gene sequences from the same organism.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

20.	In Self-organizing maps a choice is made of a number of clusters by which to organize the data.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

22.	In Genome-wide prediction of protein functions by a combinatorial method– Each point represents a protein, and branches between proteins indicate a relationship by one of several criteria indicated in the legend.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

23.	Gene identification in prokaryotic organisms is simplified by their lacking _________
A.	exons
B.	introns
C.	coding segments
D.	useful nucleotide sequences
Answer» C. coding segments

25.	Evolutionary modeling can include various types of analyses. Which is mostly not one of them?
A.	The prediction of chromosomal rearrangements
B.	Eu/Hetero-chromatin structures
C.	Duplications at gene, chromosomal and full genome level
D.	Duplications at the protein domain level
Answer» C. Duplications at gene, chromosomal and full genome level

27.	(Transposable Elements) TEs have the potential to _____ in number until they comprise a ____ proportion of the genome sequence.
A.	decrease, large
B.	decrease, micro
C.	increase, micro
D.	increase, large
Answer» E.

28.	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.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

34.	Two species that have recently diverged from a common ancestor might be expected to have a ________ set of genes and ________ chromosomes with these genes positioned along the chromosomes in the same order.
A.	distinct, similar
B.	similar, distinct
C.	similar, dissimilar
D.	similar, similar
Answer» E.

Explore topic-wise MCQs in Bioinformatics.

Which of the given statement is incorrect regarding MAGPIE?

While sequencing of The first bacterial genome—Approximately ____ of the ____ predicted genes matched genes of another species, the bacterial species E. coli K-12 that had been the subject of many years of genetic and biochemical research.

Which of the given statements is incorrect about Horizontal Gene Transfer?

Vertebrate chromosomes have long (>300 kb) regions of distinct GC richness, repeat content, and gene density, designated isochores in a model of genome organization proposing that genomes are made up of distinct segments of unique composition.

The hierarchical clustering method generates a similarity score [S(X,Y)] for all gene combinations, places the scores in a matrix, joins those genes that have the highest score, and then continues to join progressively less similar pairs.

The results of searches in separate fields may be combined to narrow down the choices.

When two proteins share a considerable degree of sequence identity throughout the sequence alignment, they are least likely to share the same function.

Sequencing of genomes depends on the assembly of a large number of DNA reads into a linear, contiguous DNA sequence.

The program returns the number of matches found and provides an opportunity to narrow this list by including more terms.

Genes that are transcribed are located in the ______

In examining the results of analysis, it is important to look for the method used the statistical significance of the result, and the overall degree of confidence in the alignments.

The sequences of satellite DNA fall into different types, each with a different repeat unit of length _____

Which of the following information is not directly obtained by microarray analysis?

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

In the program COGNITOR each protein in the proteome is used as a query of a database of protein clusters.

In case of genome sequence assembly which of the given statement is incorrect?

Each genome sequence is scanned for protein-encoding genes using gene models trained on known gene sequences from the same organism.

Which of the given statements is incorrect about Ancient Conserved Regions?

In Self-organizing maps a choice is made of a number of clusters by which to organize the data.

In cluster analysis of microarray data– For n genes, the process is repeated ________ times until a single element remains.

In Genome-wide prediction of protein functions by a combinatorial method– Each point represents a protein, and branches between proteins indicate a relationship by one of several criteria indicated in the legend.

Gene identification in prokaryotic organisms is simplified by their lacking _________

Yeast is about ______ compact than E. coli.

Evolutionary modeling can include various types of analyses. Which is mostly not one of them?

_______ of the Drosophila sequence is composed of TEs and _____ is heterochromatic regions that do not include genes.

(Transposable Elements) TEs have the potential to _____ in number until they comprise a ____ proportion of the genome sequence.

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.

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

______ can comprise a large proportion of the eukaryotic genome as ______

WU-BLAST produces P scores and BLAST (NCBI) produces E scores where _________

The designation ECa.b.c.d conveys information. Which of the following is not one of it?

Two species that have recently diverged from a common ancestor might be expected to have a ________ set of genes and ________ chromosomes with these genes positioned along the chromosomes in the same order.

The retroposons include short _________ interspersed nuclear elements (SINES).

Computational resources can facilitate the analysis of bacterial genomes.

While sequencing of the first bacterial genome–A large number of random overlapping fragments were sequenced and then a consensus sequence of the entire ______ chromosome of Hemophilus was assembled by computer.

Introns can remain at a corresponding position in a eukaryotic gene for long periods of evolutionary time.

A third category of TEs has features of both class I and class II TEs. These miniature, inverted repeat TEs (MITES) are ________ in length.

Which of the given statement is incorrect about the gene map?

_____ of the human genome comprises one particular family of the SINE Element, designated Alu (1.2 million copies).

Which of the given statement is incorrect about Clusters of functionally related genes?

In Protein 2D gel Electrophoresis, Individual proteins produced by the genome can be separated to _____ by this method and specific ones identified by various _______

Which of the given statement is incorrect about Orthologs?

Which of the given statements is incorrect about Microarray Analysis?

Other types of evidence for a relationship between two genes are also given that are not dependent in sequence similarity. Which of the following is a wrong statement?

Annotation is based on finding significant alignment to sequences of known function in database similarity searches.

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

In cluster analysis of microarray data– A node is created between the _________ scoring pair, and the gene expressed profiles of these two genes are averaged and the joined elements are weighted by the _________ of elements they contain.

The intron structure of genes in a particular eukaryote is used for predicting the location of genes of genome sequences.

While sequencing of The first bacterial genome—Approximately of the predicted genes matched genes of another species, the bacterial species E. coli K-12 that had been the subject of many years of genetic and biochemical research.

___ of the Drosophila sequence is composed of TEs and _ is heterochromatic regions that do not include genes.

(Transposable Elements) TEs have the potential to _ in number until they comprise a proportion of the genome sequence.

can comprise a large proportion of the eukaryotic genome as

Two species that have recently diverged from a common ancestor might be expected to have a set of genes and chromosomes with these genes positioned along the chromosomes in the same order.

In Protein 2D gel Electrophoresis, Individual proteins produced by the genome can be separated to _ by this method and specific ones identified by various ___

In cluster analysis of microarray data– A node is created between the _ scoring pair, and the gene expressed profiles of these two genes are averaged and the joined elements are weighted by the _ of elements they contain.

35.	The retroposons include short _________ interspersed nuclear elements (SINES).
A.	90–4000 bp long
B.	80–500 Mbp long
C.	80–300 bp long
D.	100–3000 bp long
Answer» D. 100–3000 bp long

37.	While sequencing of the first bacterial genome–A large number of random overlapping fragments were sequenced and then a consensus sequence of the entire ______ chromosome of Hemophilus was assembled by computer.
A.	8.6 x 10⁹ bp
B.	1.8 x 10⁶ bp
C.	6.9 x 10⁵ bp
D.	1.8 x 10⁴ bp
Answer» C. 6.9 x 10⁵ bp

39.	A third category of TEs has features of both class I and class II TEs. These miniature, inverted repeat TEs (MITES) are ________ in length.
A.	400 bp
B.	500 Mbp
C.	300 kbp
D.	600 kbp
Answer» B. 500 Mbp

41.	_____ of the human genome comprises one particular family of the SINE Element, designated Alu (1.2 million copies).
A.	10%
B.	20%
C.	60%
D.	40%
Answer» B. 20%

49.	In cluster analysis of microarray data– A node is created between the _________ scoring pair, and the gene expressed profiles of these two genes are averaged and the joined elements are weighted by the _________ of elements they contain.
A.	lowest, frequency
B.	average, sequence
C.	lowest, number
D.	highest, number
Answer» E.