Which of the given statements is incorrect about Cluster analysis?

A criterion for clustering proteins is the distance between each pair of sequences in a multiple sequence alignment

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

After sequencing the Hemophilus genome and Organisms were selected for sequencing based on minimum criteria. Which of the following is not one of them?

They were an important human pathogen, e.g., Mycobacterium tuberculosis (tuberculosis)

They had been subjected to a good deal of biological analysis

They were model eukaryotic organisms

They were an important human pathogen, e.g., Mycobacterium tuberculosis (tuberculosis)

They were of phylogenetic interest

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

This procedure and the algorithms are the same as those used to make a phylogenetic tree by the distance methods

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

Which of the given is wrongly matched?

Methanococcus jannaschii – Archaea

Eukaryotic genes that encode proteins are interrupted by ________

exons of varying length and but same number

exons of varying length and number

introns of varying length and number

exons of varying length and but same number

introns of varying number but same length

Each DNA or protein sequence database entry has much information, including ______

an assigned accession number(s)

Which of the given statement is untrue about functional genomics?

Sequence-based methods of gene prediction can be augmented by the types of genome comparisons that are designed to identify related genes based on common patterns of expression, evolutionary profiles, chromosomal locations, and other features

Known functions are derived from experimental evidence in molecular biology and genetic studies with model organisms

Non-Orthologous genes between biologically distinct species can be identified, and it is strong evidence for a related function

Sequence-based methods of gene prediction can be augmented by the types of genome comparisons that are designed to identify related genes based on common patterns of expression, evolutionary profiles, chromosomal locations, and other features

Genome analysis depends to a large extent on sequence analysis methods that identify gene function based on similarity between proteins of unknown function and proteins of known function

The ________ are _______ by genetic structure to retroviruses.

LTR retrotransposons, not related

Knowing ________ should be enough to find the required entry quickly.

publication date, protein name, or volume

publication date, protein name, journal name

accession number, protein name, or name of gene

publication date, protein name, or volume

properties, protein name, or title word

Which of the given statement is incorrect?

A possibility is that there is genetic variation (alleles) within each gene in a cluster of a given species and that only certain allelic combinations of different genes are compatible

In a given organism or species, genes are found in a given order that is maintained on the chromosomes from one generation to the next

Genes with a related function are frequently found to be distorted on a chromosome

A possibility is that there is genetic variation (alleles) within each gene in a cluster of a given species and that only certain allelic combinations of different genes are compatible

Clustering of related genes presumably provides an evolutionary advantage to a species

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

In all-against-all proteome comparison, each protein is used as a query in a similarity search against the remaining proteome

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)

Which of the following is incorrect about Retrieving a Specific Sequence?

For projects that require the most currently available sequences, the NR databases should be searched

It can be difficult to retrieve the sequence of a specific gene or protein simply because of the sheer number of sequences in the Gen-Bank database and the complex problem of indexing them

Other projects may benefit from the availability of better curated and annotated protein sequence databases, but not PIR and SwissProt

For projects that require the most currently available sequences, the NR databases should be searched

The genomic databases can also provide the sequence of a particular gene or protein. Protein sequences in the Genpro database are generated by automatic translation of DNA sequences

Which of the given statement is incorrect about Functional Genomics?

When two or more members of a gene family are found, rather than a single match to a known gene, the biological activity of these members may be analyzed by functional genomics to look for diversification of function in the family

Functional genomics involves the preparation of mutant or transgenic organisms with a mutant form of a particular gene usually designed to prevent expression of the gene

An abnormal properties of the mutant organism does not reveal the gene function

When two or more members of a gene family are found, rather than a single match to a known gene, the biological activity of these members may be analyzed by functional genomics to look for diversification of function in the family

A more detailed analysis of the relative amount of sequence variability in a chromosomal region within populations of closely related species can reveal the presence of genes that are under selection

Which of the given statement is incorrect about the Chromosomal Rearrangements?

In general, the order of orthologs is not well conserved in prokaryotes when the genomes have diverged sufficiently that the orthologs have < 50% identity

Comparison of the number of rearrangements in a given period of evolutionary history may vary significantly from one organism to the next

If gene A has a neighboring gene B, then if an ortholog of A occurs in another genome, there is an increased probability of an ortholog of B also occurring in the other organism

If gene A has a neighboring gene B, then if an ortholog of A occurs in another genome, the B ortholog is more likely to be a neighbor of the A ortholog of the genome of the second species if the two species are more divergent

In general, the order of orthologs is not well conserved in prokaryotes when the genomes have diverged sufficiently that the orthologs have < 50% identity

In SVMs (Support vector machines) Data points are log-transformed and normalized as in method A, where for N observations of a gene i, the log transform Xi of the expression level Ei and reference level Ri is?

Xj = \(\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)

Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_{z-2} (E_j/R_j)}}\)

Xj = \(\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)

Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,(N-1)} Log_z (E_j/R_j)}}\)

Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)

Which of the given statement is incorrect about the observations made with regard to gene order?

Order is highly conserved in closely related species

Order in closely related species becomes changed by rearrangements over evolutionary time

As more and more rearrangements occur, there will no longer be any correspondence in the order of orthologous genes on the chromosome of one organism with that of a second organism

Order is less conserved in closely related species

Which of the given statements is incorrect about Grouping 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

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

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

Orthologous pairs were first defined by the best hits in reciprocal searches

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

Which of the given statements is incorrect about Database Types?

The tables in relational database are carefully indexed and cross-referenced with each other, sometimes using additional tables, so that each item in the database has a unique set of identifying features

Relational databases are more useful in the development of biological databases

The tables in relational database are carefully indexed and cross-referenced with each other, sometimes using additional tables, so that each item in the database has a unique set of identifying features

The relational database orders data in tables made up of rows giving specific items in the database, and columns giving the features as attributes of those items

The two principal types of DBs are the relational and object-oriented databases

Which of the given features is incorrect?

TEs are present in all of the chromosomes

TEs are present in few particular chromosomes

TEs are present in all of the chromosomes

TEs can comprise a large portion of the genomes of higher eukaryotes, both plants and animals

Which of the given statements is incorrect about Microarray (or microchip) analysis?

The oligonucleotides are collectively hybridized to a labeled cDNA library prepared by reverse-transcribing mRNA from cells

It is a new technology in which all of the genes of an organism are represented by oligonucleotide sequences spread out in an 80 x 80 array on microscope slides

The oligonucleotide sequences cannot be synthesized directly on the slide

The oligonucleotides are collectively hybridized to a labeled cDNA library prepared by reverse-transcribing mRNA from cells

The amount of label binding to each oligonucleotide spot reflects the amount of mRNA in the cell

156 + Mcqs in Dna Genomic Sequencing in Bioinformatics Page 2 McqOptions

51.	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
Answer» D. A criterion for clustering proteins is the distance between each pair of sequences in a multiple sequence alignment

52.	In Proteolysis and fragment sequencing, Protein spots may be excised from a two-dimensional protein gel and subjected to a combination of amino acid sequencing and cleavage analyses using the techniques of mass spectrometry and high-pressure liquid chromatography.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

54.	Analysis of the ribosomal RNA molecules of prokaryotes and eukaryotes had led to the prediction of three main branches in the tree of life.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

55.	Most of the repetitive DNA is found near the open ends of chromosomes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

57.	A simple way to retrieve sequences of viral and other extra-chromosomal genetic elements such as organelles is through the National Center for Biotechnology Information (NCBI).
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

58.	Which of the given is wrongly matched?
A.	Escherichia coli – Bacteria
B.	Methanococcus jannaschii – Archaea
C.	Synechocystis sp. – Archaea
D.	Aquifex aeolicus – Bacteria
Answer» D. Aquifex aeolicus – Bacteria

59.	Other functional classification schemes for genes include a broader category for genes involved in the same biological process, e.g., a three-group scheme for energy-related, information-related, and communication-related genes has also been used.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

61.	Prokaryotic genomes commonly have tandem repeats of sequences and include introns in protein-coding genes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

62.	Which of the following information Sequence comparisons do not provide?
A.	Gene relationships
B.	Function history
C.	Evolutionary history
D.	Gene locations
Answer» E.

63.	In all-against-all self comparison, A comparison is made in which every protein is used as a query in a similarity search against a database composed of the rest of the proteome, and the significant matches are identified by a low expect value.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

64.	Each DNA or protein sequence database entry has much information, including ______
A.	an assigned accession number(s)
B.	source organism
C.	name of locus
D.	reference number type(s)
Answer» E.

77.	The Common Object Request Broker Architecture (CORBA) is the Object Management Group’s interface for objects.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

66.	Pseudogenes are DNA sequences that were derived from distinct genes but which have acquired mutations that are deleterious to function in the same period of time.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

67.	The ________ are _______ by genetic structure to retroviruses.
A.	STR retrotransposons, related
B.	LTR retrotransposons, related
C.	STR transposons, related
D.	LTR retrotransposons, not related
Answer» C. STR transposons, related

69.	An all-against-all analysis requires first making a database of the proteome. This database is then sequentially searched by each individual protein sequence of the proteome using a rapid database similarity search tool such as _______
A.	XPBLAST
B.	WU-BLAST
C.	BLAST
D.	FASTA
Answer» B. WU-BLAST

73.	In nondividing cells, a mixture of lightly and darkly stained chromosomal regions called euchromatin and heterochromatin respectively, are observed.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

74.	GeneQuiz focuses on deriving a predicted protein function, based on a variety of available evidence, including the evaluation of the similarity to the closest homolog in a database.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

75.	Annotation involves identifying open reading frames in the genome sequence.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

76.	New gene functions are thought to be gained by duplication of an existing gene creating two tandem copies.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

78.	The FASTA format is readily converted into other formats and also is smaller and simpler.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

85.	The higher the E value, the more significant the alignment between a pair of matching sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

86.	The chromosomes comprised linear DNA molecules in a tightly compact form that was wrapped around protein complexes, called the nucleosome.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Which of the given statements is incorrect about Cluster analysis?

In Proteolysis and fragment sequencing, Protein spots may be excised from a two-dimensional protein gel and subjected to a combination of amino acid sequencing and cleavage analyses using the techniques of mass spectrometry and high-pressure liquid chromatography.

After sequencing the Hemophilus genome and Organisms were selected for sequencing based on minimum criteria. Which of the following is not one of them?

Analysis of the ribosomal RNA molecules of prokaryotes and eukaryotes had led to the prediction of three main branches in the tree of life.

Most of the repetitive DNA is found near the open ends of chromosomes.

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

A simple way to retrieve sequences of viral and other extra-chromosomal genetic elements such as organelles is through the National Center for Biotechnology Information (NCBI).

Which of the given is wrongly matched?

Other functional classification schemes for genes include a broader category for genes involved in the same biological process, e.g., a three-group scheme for energy-related, information-related, and communication-related genes has also been used.

Eukaryotic genes that encode proteins are interrupted by ________

Prokaryotic genomes commonly have tandem repeats of sequences and include introns in protein-coding genes.

Which of the following information Sequence comparisons do not provide?

In all-against-all self comparison, A comparison is made in which every protein is used as a query in a similarity search against a database composed of the rest of the proteome, and the significant matches are identified by a low expect value.

Each DNA or protein sequence database entry has much information, including ______

Which of the given statement is untrue about functional genomics?

Pseudogenes are DNA sequences that were derived from distinct genes but which have acquired mutations that are deleterious to function in the same period of time.

The ________ are _______ by genetic structure to retroviruses.

Knowing ________ should be enough to find the required entry quickly.

An all-against-all analysis requires first making a database of the proteome. This database is then sequentially searched by each individual protein sequence of the proteome using a rapid database similarity search tool such as _______

Which of the given statement is incorrect?

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

Which of the following is incorrect about Retrieving a Specific Sequence?

In nondividing cells, a mixture of lightly and darkly stained chromosomal regions called euchromatin and heterochromatin respectively, are observed.

GeneQuiz focuses on deriving a predicted protein function, based on a variety of available evidence, including the evaluation of the similarity to the closest homolog in a database.

Annotation involves identifying open reading frames in the genome sequence.

New gene functions are thought to be gained by duplication of an existing gene creating two tandem copies.

The Common Object Request Broker Architecture (CORBA) is the Object Management Group’s interface for objects.

The FASTA format is readily converted into other formats and also is smaller and simpler.

Which of the given statement is incorrect about Functional Genomics?

Which of the given statement is incorrect about the Chromosomal Rearrangements?

In SVMs (Support vector machines) Data points are log-transformed and normalized as in method A, where for N observations of a gene i, the log transform Xi of the expression level Ei and reference level Ri is?

Which of the given statement is incorrect about the observations made with regard to gene order?

Which of the given statements is incorrect about Grouping Sequences?

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

The higher the E value, the more significant the alignment between a pair of matching sequences.

The chromosomes comprised linear DNA molecules in a tightly compact form that was wrapped around protein complexes, called the nucleosome.

In Metabolic pathways and regulation, as genes are identified in a new genome sequence, some will be found that are known to act sequentially in a metabolic pathway or to have a known role in gene regulation in other organisms.

Which of the given statements is incorrect about Database Types?

TEs (Transposable Elements) can at most comprise one-fourth of the genome sequence.

Screening the predicted protein sequences against ______ library confirms the prediction and expression of the gene.

Which of the given features is incorrect?

Minisatellites are made up of repeat units of up to ____ and microsatellites compose of repeat units of ____ or less.

The human genome contains about _________ of class II of elements that probably predate human evolution (Smit 1996).

Which of the given statements is incorrect about Microarray (or microchip) analysis?

The translated sequence can then be compared to a database of protein sequences with the hope of finding a strong similarity to a protein of known function, and hence to identify the function of the cloned EST.

Using cDNA sequence with the __________ it is much simpler to locate protein-encoding sequences in these molecules.

An important development for computational purposes was the decision by Craig Venter to prepare databases of partial sequences of the expressed genes, called expressed sequence tags or ESTs.

cDNA libraries have been prepared that have the same sequences as the mRNA molecules produced by organisms, or else cDNA copies are sequenced directly by RT-PCR (copying of mRNA by reverse transcriptase followed by sequencing of the cDNA copy by the polymerase chain reaction).

Two common goals in sequence analysis are to identify sequences that encode proteins, which determine all cellular metabolisms, and to discover sequences that regulate the expression of genes or other cellular processes.

Investigators are encouraged to submit their newly obtained sequences directly to a member of the International Nucleotide Sequence Database Collaboration, such as the NCBI, DDBJ, and EMBL.

The __ are _ by genetic structure to retroviruses.

Minisatellites are made up of repeat units of up to and microsatellites compose of repeat units of or less.

90.	Screening the predicted protein sequences against ______ library confirms the prediction and expression of the gene.
A.	expressed sequence tag (EST)
B.	tags
C.	palindromes
D.	proteomes
Answer» B. tags

92.	Minisatellites are made up of repeat units of up to ____ and microsatellites compose of repeat units of ____ or less.
A.	25 bp, 10 bp
B.	70 bp, 6 bp
C.	80 bp, 9 bp
D.	25 bp, 4 bp
Answer» E.

93.	The human genome contains about _________ of class II of elements that probably predate human evolution (Smit 1996).
A.	2,000 copies
B.	200,000 copies
C.	2,00,00,000 copies
D.	20,00,000 copies
Answer» C. 2,00,00,000 copies

96.	Using cDNA sequence with the __________ it is much simpler to locate protein-encoding sequences in these molecules.
A.	exons taken out
B.	exons removed
C.	introns added
D.	introns removed
Answer» E.

100.	Investigators are encouraged to submit their newly obtained sequences directly to a member of the International Nucleotide Sequence Database Collaboration, such as the NCBI, DDBJ, and EMBL.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False