Which of the following is untrue regarding the Predicting Interactions Based on Domain Fusion?

It is based on gene fusion events

Predicting protein–protein interactions is called the “Rosetta stone” method

A fused protein often reveals relationships between its domain components

A fused protein doesn’t necessarily reveal about the relationships between its domain components

Which of the following is untrue regarding the drawbacks of expressed sequence tags (ESTs)?

They are often of lowquality because they are automatically generated without verification

Many bases are ambiguously determined, represented by N’s

Frame shift errors and artifactual stop codons are some common errors

Despite of all the failures, the translation the sequences is smooth

Which of the following is incorrect about Hierarchical Clustering?

It produces a treelike structure that represents a hierarchy or relative relatedness of data groups

The tree-branching pattern illustrates a higher degree of relationship between related gene groups

It is not similar to the distance phylogenetic tree-building method

It produces a treelike structure that represents a hierarchy or relative relatedness of data groups

In the tree leaves, similar gene expression profiles are placed more closely together than dissimilar gene expression profiles

Which of the following is untrue regarding TIGR Gene Indices?

It is an EST database that uses a different clustering method from UniGene

It is an EST database that the similar type of clustering method from UniGene

It is an EST database that uses a different clustering method from UniGene

It compiles data from dbEST, GenBank mRNA and genomic DNA data, and TIGR’s own sequence databased Sequences are only clustered if they are more than 95% identical for over a fortynucleotide region in pairwise comparisons

Which of the following is incorrect about k-Means Clustering?

It classifies data through a single step partition

k-means clustering produces a dendrogram

It classifies data through a single step partition

In this method, data are partitioned into k-clusters, which are prespecified at the outset

which of the following is incorrect about Oligonucleotide Design in A microarray?

DNA microarrays are generated by fixing oligonucleotides onto a solid support

The oligonucleotide array slide represents thousands of preselected genes from an organism

The length of oligonucleotides is typically in the range of twenty-five to seventy bases long

The oligonucleotides don’t react with cDNA samples

Which of the following is untrue regarding EST Index Construction?

The goal of the EST databases is to improve the quality of the sequence information so the data can be used to extract full-length cDNAs

The goal of the EST databases is to organize and consolidate the largely redundant EST data

The process includes a preprocessing step that removes masks repeats

There is no screening of vector contaminants

The goal of the EST databases is to improve the quality of the sequence information so the data can be used to extract full-length cDNAs

Which of the following is incorrect regarding Mass Spectrometry Protein Identification?

Proteins can be identified and characterized using MS

The proteolysis doesn’t generate a pattern according to molecular weight

Proteins can be identified and characterized using MS

The proteins from a two dimensional gel system are first digested in situ with a protease

Protein spots of interest are excised from the two-dimensional gel

Which of the following is untrue regarding SAGE?

Unlike EST sampling, SAGE is more quantitative in determining mRNA expression in a cell

It stands for Serial analysis of gene expression

It is another high throughput, sequence-based approach for global gene expression profile analysis

It stands for Squared analysis of gene expression

Unlike EST sampling, SAGE is more quantitative in determining mRNA expression in a cell

Which of the following is an incorrect statement about SignalP?

It is a web-based program that predicts subcellular localization signals

It uses both neural networks and HMMs

Which of the following is untrue about Lateral gene transfer?

There is exchange of genetic materials between species

It is also known as vertical gene transfer

There is exchange of genetic materials between species

It mainly occurs among prokaryotic organisms when foreign genes are acquired through mechanisms

It is one of the examples is transformation

In hierarchical genome sequencing approach, based on the results of _______ mapping _______of the BAC clones on a chromosome can be determined.

physical, the locations and orders

cytological, only the locations

Which of the following is untrue about comparative genomics?

It doesn’t help to reveal the extent of conservation among genomes

It is comparison of whole genomes from different organisms

It includes comparison of gene number, gene location, and gene content from these genomes

It provides insights into the mechanism of genome evolution and gene transfer among genomes

It doesn’t help to reveal the extent of conservation among genomes

Which of the following is untrue about Whole Genome Alignment?

It be accomplished through direct genome comparison or genome alignment

This helps to reveal the presence of conserved functional elements

It doesn’t help to understand sequence conservation between genomes

It be accomplished through direct genome comparison or genome alignment

The alignment at the genome level is fundamentally no different from the basic sequence alignment

A way to discern lateral gene transfer is through phylogenetic analysis, referred to as an ‘among-genome’ approach, which can be used to discover __________

recent lateral gene transfer events but almost negligible ancient events

recent lateral gene transfer events

ancient lateral gene transfer events

both recent and ancient lateral gene transfer events

Which of the following is untrue regarding the predicting Interactions Based on Phylogenetic Information?

This method detects the co-presence or co-absence of orthologs across a number of genomes

Proteins do not operate as a complex

This method detects the co-presence or co-absence of orthologs across a number of genomes

Protein interactions can be predicted using phylogenetic profiles

Phylogenetic profile are defined as patterns of gene pairs that are concurrently present or absent across genomes

Which of the following is incorrect about Data Collection?

The most common type of microarray protocol is the two-color microarray

The two-color microarray uses multiple dyes at times

The most common type of microarray protocol is the two-color microarray

The cDNAs are obtained by extracting total RNA or mRNA from tissues or cells and incorporating fluorescent dyes in the DNA strands during the cDNA biosynthesis

The expression of genes is measured via the signals from cDNAs hybridizing with the specific oligonucleotide probes on the microarray

Which of the following is incorrect regarding Mascot and ProFound?

Mascot is a web server that identifies proteins based on peptide mass fingerprints, sequence entries, or raw MS/MS data from one or more peptides

ProFound is a web server with a set of interconnected programs

ProFound searches a protein sequence database using MS fingerprinting information

Bayesian algorithm is not involved in ProFound

Mascot is a web server that identifies proteins based on peptide mass fingerprints, sequence entries, or raw MS/MS data from one or more peptides

Which of the following is incorrect regarding the Protein Identification through Database Searching?

The purpose of the database search is to find exact or nearly exact matches

MS characterization of proteins is highly dependent on bioinformatic analysis

Bioinformatics programs can be used to search for the identity of a protein in a database of theoretically digested proteins

Even in reality, the protease digestion is always perfect in MS

The purpose of the database search is to find exact or nearly exact matches

Which of the following is untrue regarding the STRING?

It is based on combined evidence of gene linkage, gene fusion and phylogenetic profiles

Search Tool for the Retrieval of Interacting Genes/Proteins

Functional associations include only the direct protein-protein interactions

It is based on combined evidence of gene linkage, gene fusion and phylogenetic profiles

It is a web server that predicts gene and protein functional associations

Which of the following is untrue about cytologic maps?

They cannot be directly observed under microscope

They can be viewed on stained chromosomes

They can be directly observed under microscope

In a statistical learning process called support vector machine (SVM), a hyperplane is _____

nonlinear mathematical function

a linear or nonlinear mathematical function

nonlinear mathematical function

exponential mathematical function

113 + Mcqs in Genomics and Proteomics in Bioinformatics Page 1 McqOptions

1.	Cysteine doesn’t make predictions by building profiles.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

2.	A disulfide bridge is a unique type of _____ modification in which _____ bonds are formed between cysteine residues.
A.	posttranslational, covalent
B.	translational, covalent
C.	translational, ionic
D.	posttranslational, ionic
Answer» B. translational, covalent

3.	Once the proteins are translocated within the organelles, protease cleavage takes place to remove the signal sequences and generate mature proteins.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

5.	GenBank has a special EST database, dbEST that contains EST collections for a large number of organisms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

6.	It has been estimated that up to 11% of cDNA clones may be chimeric.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

9.	To minimize false-positive results, a statistical learning process called support vector machine (SVM) can be used to increase the specificity of prediction.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

10.	Electrospray ionization MS and matrix-assisted laser desorption ionization (MALDI) MS only differ in the ionization procedure used.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

13.	It is important to use bioinformatics tools to predict sites for posttranslational modifications based on specific protein sequences. However, prediction of such modifications can often be difficult because the short lengths of the sequence motifs associated with certain modifications.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

18.	Which of the following is an incorrect statement about SignalP?
A.	It only uses neural networks
B.	It only uses HMMs
C.	It is a web-based program that predicts subcellular localization signals
D.	It uses both neural networks and HMMs
Answer» C. It is a web-based program that predicts subcellular localization signals

19.	TIGR TM4 is a suite of multiplatform programs for analyzing microarray data.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

20.	Only Advanced neural networks are used to discern long-distance pairwise interactions among cysteine residues.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

22.	Coregenes is a web-based program that determines a ________ set of genes based on comparison of ________ small genomes.
A.	vast, four
B.	core, fifteen
C.	core, four
D.	vast, fifteen
Answer» D. vast, fifteen

23.	If the bait and prey proteins _______ they bring the DNA-binding and trans-activation domains in such close proximity that they reconstitute the function of the transcription activator, turning ____ the expression of a reporter gene as a result. Which of the following is not the correct pair of blanks?
A.	physically interact, on
B.	do not interact, on
C.	do not interact, off
D.	stop interacting, off
Answer» C. do not interact, off

33.	The shotgun approach does not require knowledge of physical mapping of the clone fragments, but rather a robust computer assembly program to join the pieces of random fragments into a single, whole-genome sequence.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

35.	The justification behind Rosetta stone method is that when two domains are fused in a single protein, they have to be in _______ proximity to perform a common function.
A.	distant
B.	close
C.	extremely distant
D.	extremely close
Answer» E.

21.	ExPASY is a comprehensive proteomics web server with a suite of programs for searching peptide information from the SWISS-PROT and TrEMBL databases.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

25.	Genes involved in the same metabolic pathway tend to be clustered among phylogenetically diverse organisms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

26.	In hierarchical genome sequencing approach, based on the results of _______ mapping _______of the BAC clones on a chromosome can be determined.
A.	physical, the locations and orders
B.	physical, only the locations
C.	cytological, only the locations
D.	physical, only the orders
Answer» B. physical, only the locations

27.	Comparing two-dimensional gel images from various experiments can sometimes pose a challenge because the gels, unlike DNA microarrays, may shrink or warp.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

28.	Chloroplast localization signals consist of two adjacent signal peptides, one for targeting the proteins to the stromaportion of the chloroplast before being cleaved and the other for targeting the remaining portion of the proteins to the thylakoids.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

30.	Accurate prediction of _____ bonds may also help to predict the _____ dimensional structure of the protein of interest.
A.	nitrogen, two
B.	nitrogen, three
C.	disulfide, three
D.	oxygen, three
Answer» D. oxygen, three

36.	When the two domains are located in two different proteins, to preserve the same functionality, their close proximity and interaction have to be preserved as well.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

37.	In medical applications, the ultimate goal of gene mapping is to disease genes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

38.	One of the fundamental events that occur in meiosis is crossing over in which homologous chromosomes exchange segments causing a reshuffling of genes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

40.	Cytologic maps can be considered to be of _____ resolution and hence somewhat ______ physical maps.
A.	very high, inaccurate
B.	very low, accurate
C.	very high, accurate
D.	very low, inaccurate
Answer» E.

Explore topic-wise MCQs in Bioinformatics.

Cysteine doesn’t make predictions by building profiles.

A disulfide bridge is a unique type of _____ modification in which _____ bonds are formed between cysteine residues.

Once the proteins are translocated within the organelles, protease cleavage takes place to remove the signal sequences and generate mature proteins.

Which of the following is untrue regarding the Predicting Interactions Based on Domain Fusion?

GenBank has a special EST database, dbEST that contains EST collections for a large number of organisms.

It has been estimated that up to 11% of cDNA clones may be chimeric.

Which of the following is untrue regarding the drawbacks of expressed sequence tags (ESTs)?

Which of the following is incorrect about Hierarchical Clustering?

To minimize false-positive results, a statistical learning process called support vector machine (SVM) can be used to increase the specificity of prediction.

Electrospray ionization MS and matrix-assisted laser desorption ionization (MALDI) MS only differ in the ionization procedure used.

Which of the following is untrue regarding TIGR Gene Indices?

Which of the following is incorrect about k-Means Clustering?

It is important to use bioinformatics tools to predict sites for posttranslational modifications based on specific protein sequences. However, prediction of such modifications can often be difficult because the short lengths of the sequence motifs associated with certain modifications.

which of the following is incorrect about Oligonucleotide Design in A microarray?

Which of the following is untrue regarding EST Index Construction?

Which of the following is incorrect regarding Mass Spectrometry Protein Identification?

Which of the following is untrue regarding SAGE?

Which of the following is an incorrect statement about SignalP?

TIGR TM4 is a suite of multiplatform programs for analyzing microarray data.

Only Advanced neural networks are used to discern long-distance pairwise interactions among cysteine residues.

ExPASY is a comprehensive proteomics web server with a suite of programs for searching peptide information from the SWISS-PROT and TrEMBL databases.

Coregenes is a web-based program that determines a ________ set of genes based on comparison of ________ small genomes.

Which of the following is untrue about Lateral gene transfer?

Genes involved in the same metabolic pathway tend to be clustered among phylogenetically diverse organisms.

In hierarchical genome sequencing approach, based on the results of _______ mapping _______of the BAC clones on a chromosome can be determined.

Comparing two-dimensional gel images from various experiments can sometimes pose a challenge because the gels, unlike DNA microarrays, may shrink or warp.

Chloroplast localization signals consist of two adjacent signal peptides, one for targeting the proteins to the stromaportion of the chloroplast before being cleaved and the other for targeting the remaining portion of the proteins to the thylakoids.

Which of the following is untrue about comparative genomics?

Accurate prediction of _____ bonds may also help to predict the _____ dimensional structure of the protein of interest.

Which of the following is untrue about Whole Genome Alignment?

A way to discern lateral gene transfer is through phylogenetic analysis, referred to as an ‘among-genome’ approach, which can be used to discover __________

The shotgun approach does not require knowledge of physical mapping of the clone fragments, but rather a robust computer assembly program to join the pieces of random fragments into a single, whole-genome sequence.

Which of the following is untrue regarding the predicting Interactions Based on Phylogenetic Information?

The justification behind Rosetta stone method is that when two domains are fused in a single protein, they have to be in _______ proximity to perform a common function.

When the two domains are located in two different proteins, to preserve the same functionality, their close proximity and interaction have to be preserved as well.

In medical applications, the ultimate goal of gene mapping is to disease genes.

One of the fundamental events that occur in meiosis is crossing over in which homologous chromosomes exchange segments causing a reshuffling of genes.

Which of the following is incorrect about Data Collection?

Cytologic maps can be considered to be of _____ resolution and hence somewhat ______ physical maps.

Which of the following is incorrect regarding Mascot and ProFound?

ExPASY contains a number of programs to determine posttranslational modifications based on MS molecular mass data.

Which of the following is incorrect regarding the Protein Identification through Database Searching?

Which of the following is untrue regarding the STRING?

TargetP is a neural network-based program, similar to SignalP.

Which of the following is untrue about cytologic maps?

In Predicting Interactions Based on Gene Neighbors if a certain gene linkage is found to be indeed conserved across divergent genomes, it can be used as a strong indicator of formation of an operon that encodes proteins that are functionally and even physically coupled.

In a statistical learning process called support vector machine (SVM), a hyperplane is _____

The PCR amplification step involved in the SAGE procedure means that it requires a large quantity of sample mRNA.

The signal sequences have a _________ consensus but contain some specific features. They all have a ______ core region preceded by one or more positively charged residues.

A disulfide bridge is a unique type of _ modification in which _ bonds are formed between cysteine residues.

Coregenes is a web-based program that determines a set of genes based on comparison of small genomes.

In hierarchical genome sequencing approach, based on the results of _ mapping _of the BAC clones on a chromosome can be determined.

Accurate prediction of _ bonds may also help to predict the _ dimensional structure of the protein of interest.

Cytologic maps can be considered to be of _ resolution and hence somewhat __ physical maps.

The signal sequences have a ___ consensus but contain some specific features. They all have a core region preceded by one or more positively charged residues.

46.	Which of the following is untrue about cytologic maps?
A.	They cannot be directly observed under microscope
B.	They refer to banding patterns
C.	They can be viewed on stained chromosomes
D.	They can be directly observed under microscope
Answer» B. They refer to banding patterns

50.	The signal sequences have a _________ consensus but contain some specific features. They all have a ______ core region preceded by one or more positively charged residues.
A.	weak, hydrophilic
B.	weak, hydrophobic
C.	strong, hydrophilic
D.	strong, hydrophilic
Answer» C. strong, hydrophilic