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Bioinformatics

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Quiz on Bioinformatics, created by lauren beck on 19/01/2020.
lauren beck
Quiz by lauren beck, updated more than 1 year ago
lauren beck
Created by lauren beck almost 5 years ago
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Resource summary

Question 1

Question
Which of the following are sequence elements that algorithms can exploit to search for genes in a prokaryotic genome?
Answer
  • TFIIB recognition element
  • TATA box at -10
  • ATG start codon
  • STOP codon
  • downstream core promoter element at +30
  • initiator element around transcription start site

Question 2

Question
[blank_start]Sanger sequencing[blank_end] is an example of a first generation sequencing technology
Answer
  • Sanger sequencing

Question 3

Question
Sanger sequencing has been automated by fluorescent labelling
Answer
  • True
  • False

Question 4

Question
Which of the following are advantages of sanger sequencing?
Answer
  • high accuracy
  • good for short sequences
  • high throughput
  • cheap
  • long read length

Question 5

Question
select the technologies that are second generation sequencing methods
Answer
  • Sanger
  • 454 pyrosequencing
  • Ilumina
  • Ion torrent
  • nanopore
  • PacBio

Question 6

Question
Which of the following are limitations of 454 pyrosequencing?
Answer
  • slow sample preparation
  • lower throughput than sanger
  • shorter read lengths than sanger
  • homopolymer errors

Question 7

Question
A homopolymer error is a problem with base calling which there are multiple bases in a row as the signal does not increase with linearity
Answer
  • True
  • False

Question 8

Question
454 pyrosequencing and ion torrent use solid-phase bridge PCR
Answer
  • True
  • False

Question 9

Question
Ion torrent detects the incorporation of a base based on [blank_start]light[blank_end] whereas 454 pyrosequencing detects the incorporation of a base based on [blank_start]pH[blank_end]
Answer
  • pH
  • light

Question 10

Question
What are the advantages of third generation sequencing technologies?
Answer
  • High accuracy
  • high throughput
  • longer read length
  • Low cost
  • minimal sample preparation

Question 11

Question
[blank_start]human[blank_end] [blank_start]genome[blank_end] [blank_start]project[blank_end] [blank_start]encode[blank_end] and [blank_start]1000[blank_end] [blank_start]genomes[blank_end] [blank_start]project[blank_end] are all examples of large scale genome sequencing projects
Answer
  • human
  • genome
  • project
  • encode
  • 1000
  • genomes
  • project

Question 12

Question
[blank_start]shotgun[blank_end] [blank_start]sequencing[blank_end] is the most common sequencing approach for whole genomes
Answer
  • shotgun
  • sequencing

Question 13

Question
a [blank_start]contig[blank_end] is a set of overlapping DNA fragments that together represent a consensus region of DNA
Answer
  • contig
  • scaffold
  • read
  • coverage

Question 14

Question
the de bruijn graph method is a greedy method of assembly
Answer
  • True
  • False

Question 15

Question
[blank_start]k[blank_end] is the parameter used in the de bruijn graph assembly algorithm
Answer
  • k

Question 16

Question
sequence assembly can be...
Answer
  • ab initio
  • de novo
  • read mapping

Question 17

Question
Which of the following are de bruijn graph sequence assemblers?
Answer
  • Celera
  • GigAssembler
  • Velvet
  • SPAdes

Question 18

Question
Genomes always need to be finished
Answer
  • True
  • False

Question 19

Question
hybrid sequencing is an effective way of closing gaps in genome assembly as different technologies are biased in sequencing in different ways
Answer
  • True
  • False

Question 20

Question
in the equation N = (a x g) / L N is the [blank_start]reads[blank_end] a is the [blank_start]coverage[blank_end] g is the genome length and L is the read length
Answer
  • reads
  • coverage
  • genome length
  • read length
  • coverage
  • reads
  • genome length
  • read length

Question 21

Question
Which of the following are examples of challenges faced during sequence assembly?
Answer
  • sequencing errors
  • shotgun fragmenting is not random
  • repeated regions
  • computational power
  • throughput
  • cost

Question 22

Question
Why can't BLAST be used for short read mapping to assemble our reads using a reference genome?
Answer
  • it costs too much and is highly inaccurate
  • it is not compatible
  • it takes too long and is not good at finding close matches

Question 23

Question
when might short-read mapping be beneficial to use?
Answer
  • for RNA-sequencing experiments
  • for chipping experiments
  • to assemble a whole genome
  • to find open reading frames

Question 24

Question
[blank_start]Burrows[blank_end]-[blank_start]wheeler[blank_end] is the name of the algorithm which is used by mapping alignment packages such as Bowtie in order to convert the genome into a different format so matches can be easily found
Answer
  • Burrows
  • wheeler

Question 25

Question
We always need to assemble the genome in metagenomics experiments
Answer
  • True
  • False

Question 26

Question
raw sequencing data from sequencing experiments are saved in the sequence read archive
Answer
  • True
  • False

Question 27

Question
annotated sequence data from sequencing experiments are saved in GenBank and EMBL
Answer
  • True
  • False

Question 28

Question
Which of the following are legitimate methods of assessing a sequence assembly?
Answer
  • the N50 statistic
  • principle component analysis
  • average gap size
  • average number of gaps per scaffold
  • coverage
  • hierarchical clusterin

Question 29

Question
the N50 statistic is the length of the smallest contig in the set that contains the fewest contigs whose combined length represents 50% of the assembly
Answer
  • True
  • False

Question 30

Question
sequence annotation involves identifying...
Answer
  • read lengths
  • coverage
  • CDSs
  • promoters
  • ribosome binding sites
  • introns
  • exons

Question 31

Question
gene prediction involves finding UTRs and alternative splice isoforms
Answer
  • True
  • False

Question 32

Question
what are the 2 major approaches for gene finding?
Answer
  • ab initio
  • comparative proteomics
  • comparative genomics
  • de novo

Question 33

Question
ab initio gene finding approaches are more accurate for eukaryotes than prokaryotes
Answer
  • True
  • False

Question 34

Question
the gene finding tools Glimmer and GeneScan use [blank_start]hidden[blank_end] [blank_start]markov[blank_end] models
Answer
  • hidden
  • markov

Question 35

Question
which of the following make eukaryotic gene finding more difficult than prokaryotic gene finding?
Answer
  • high number of repeats
  • introns
  • exons
  • highly compact
  • alternative splicing

Question 36

Question
What measures can be used to assess gene prediction?
Answer
  • sensitivity
  • specificity
  • accuracy
  • N50 statistic

Question 37

Question
There is a trade-off when it comes to the specificity and sensitivity of gene prediction tools
Answer
  • True
  • False

Question 38

Question
[blank_start]prokka[blank_end] is a genome annotation pipeline good for prokaryotes and small eukaryotes
Answer
  • prokka
  • genescan
  • glimmer
  • genie

Question 39

Question
order the types of mutation in terms of relative frequency: 1. [blank_start]point[blank_end] 2. [blank_start]deletion[blank_end] 3. [blank_start]duplication[blank_end] 4. [blank_start]inversion[blank_end] 5. [blank_start]insertion[blank_end] 6. [blank_start]translocation[blank_end]
Answer
  • point
  • deletion
  • inversion
  • insertion
  • translocation
  • duplication
  • deletion
  • point
  • insertion
  • inversion
  • duplication
  • translocation
  • duplication
  • point
  • deletion
  • inversion
  • insertion
  • translocation
  • inversion
  • insertion
  • point
  • deletion
  • translocation
  • duplication
  • insertion
  • inversion
  • translocation
  • duplication
  • point
  • deletion
  • translocation
  • inversion
  • insertion
  • duplication
  • point
  • deletion

Question 40

Question
silent, missense and nonsense are all types of [blank_start]point[blank_end] mutation
Answer
  • point

Question 41

Question
nonsense mutations can be conservative or non-conservative (similar AA or not)
Answer
  • True
  • False

Question 42

Question
introns, intergenic regions and pseudogenes are highly conserved and intolerant to change
Answer
  • True
  • False

Question 43

Question
Gene duplicates experience relaxed evolutionary constraints
Answer
  • True
  • False

Question 44

Question
when does gene duplication occur in bacteria?
Answer
  • in response to favourable conditions
  • in response to stress
  • in response to an internal stimulus
  • linearly over evolutionary time

Question 45

Question
[blank_start]duplication[blank_end] is an essential mutation for evolutionary change to occur in eukaryotes
Answer
  • duplication
  • point mutation
  • inversion
  • insertion
  • deletion

Question 46

Question
gene duplication can lead to [blank_start]nonfunctionalisation[blank_end] [blank_start]neofunctionalisation[blank_end] or [blank_start]subfunctionalisation[blank_end]
Answer
  • nonfunctionalisation
  • neofunctionalisation
  • subfunctionalisation

Question 47

Question
which of the following are sources of variation in prokaryotes?
Answer
  • lateral gene transfer
  • endosymbiosis
  • mutations

Question 48

Question
genes that share a common ancestor are said to be what?
Answer
  • homologs
  • paralogs
  • orthologs
  • xenologs

Question 49

Question
genes that have diverged as a result of speciation are said to be what?
Answer
  • homologs
  • orthologs
  • paralogs
  • xenologs

Question 50

Question
genes within the same genome created as a result of gene duplication are said to be what?
Answer
  • homologs
  • orthologs
  • paralogs
  • xenologs

Question 51

Question
homology is a measure of similarity
Answer
  • True
  • False

Question 52

Question
which of the following are simplistic measure of similarity when it comes to measuring sequence similarity?
Answer
  • hamming distance
  • sequence identity
  • levenshtein distance
  • PAM250
  • BLOSUM62

Question 53

Question
what kind of mutations are more common?
Answer
  • point mutations
  • translocation mutations
  • amino acid substitutions tend to be conservative
  • single nucleotide or amino acid deletions
  • successive deletions of bases or amino acids
  • transversion mutations
  • transition mutations

Question 54

Question
PAM and BLOSUM are example of [blank_start]substitution[blank_end] [blank_start]matrices[blank_end]
Answer
  • substitution
  • matrices

Question 55

Question
1 PAM is 1% similarity
Answer
  • True
  • False

Question 56

Question
PAM is better for [blank_start]global[blank_end] alignments whilst BLOSUM is better for [blank_start]local[blank_end] alignments
Answer
  • global
  • local

Question 57

Question
BLOSUM matrices are derived from the [blank_start]BLOCKS[blank_end] database
Answer
  • BLOCKS

Question 58

Question
A higher PAM matrix will find weaker, longer alignments and a BLOSUM matrix with a higher number are better for similar sequences
Answer
  • True
  • False

Question 59

Question
A local alignment tries to align all the residues in a sequence
Answer
  • True
  • False

Question 60

Question
Dynamic programming is used for [blank_start]exact[blank_end] alignment methods
Answer
  • exact

Question 61

Question
Needleman-Wunsch is a [blank_start]global[blank_end] alignment algorithm
Answer
  • global

Question 62

Question
Smith-waterman is a local alignment algorithm
Answer
  • True
  • False

Question 63

Question
The trajectory refers to the traceback arrows in a trajectory table
Answer
  • True
  • False

Question 64

Question
BLAST and FASTA are examples of [blank_start]heuristic[blank_end] alignment methods
Answer
  • heuristic

Question 65

Question
Exact alignment methods are not guaranteed to find an optimal solution
Answer
  • True
  • False

Question 66

Question
K-tuple alignment methods are a family of approximate alignment methods, and BLAST is part of the family
Answer
  • True
  • False

Question 67

Question
a [blank_start]heuristic[blank_end] approach is taken with multiple sequence alignment because an exact approach has complexity O(L^N)
Answer
  • heuristic

Question 68

Question
progressive, iterative and statistical are all approaches used for [blank_start]MSA[blank_end]
Answer
  • MSA

Question 69

Question
Which of the following are examples of progressive alignment algorithms?
Answer
  • T-coffee
  • Clustal omega
  • Clustal W
  • Muscle

Question 70

Question
Which of the following algorithms takes a hybrid approach for multiple sequence alignment?
Answer
  • T-coffee
  • Muscle
  • Clustal omega
  • Clustal W

Question 71

Question
A [blank_start]motif[blank_end] is part of a protein sequence associated with a particular biological function
Answer
  • motif

Question 72

Question
A [blank_start]pattern[blank_end] is a qualitative description of a motif A [blank_start]profile[blank_end] is a quantitative description of a motif
Answer
  • profile
  • pattern
  • pattern
  • profile

Question 73

Question
Which of the following databases describe motifs in terms of pattern and profile?
Answer
  • Pfam
  • PROSITE
  • InterPro
  • GeneBank
  • EMBL
  • BLOCKS

Question 74

Question
PSI-BLAST is more powerful than BLAST for picking up distant relationships between sequences
Answer
  • True
  • False

Question 75

Question
in phylogenetics, masking an alignment involved looking for regions or conservation and removing data that does not appear homologous
Answer
  • True
  • False

Question 76

Question
Which of the following are examples of distance-based tree building methods?
Answer
  • Maximum likelihood
  • Maximum parsimony
  • UPGMA
  • WPGMA
  • Bayesian inference

Question 77

Question
[blank_start]Bootstrap[blank_end] [blank_start]values[blank_end] can be added to branches in phylogenetic trees to summarise the degree of certainty for a given branching
Answer
  • Bootstrap
  • values

Question 78

Question
[blank_start]WPGMA[blank_end] uses a flat average whilst UPGMA uses a weighted average that takes into account the number of taxa in a group
Answer
  • WPGMA

Question 79

Question
microarrays and RNA-sequencing are examples of what kind of experiments?
Answer
  • genomics
  • transcriptomics
  • proteomics
  • phylogenetics

Question 80

Question
[blank_start]normalisation[blank_end] aims to remove technical variation existing in microarray experiments
Answer
  • normalisation

Question 81

Question
Which of the following are methods for quality control to remove outliers from microarray experiments?
Answer
  • N50 statistic
  • hierarchical clustering
  • normalisation
  • principle component analysis
  • probeset QC
  • multiple testing correction

Question 82

Question
following a microarray experiment, probeset QC removes noise and uninformative data points (i.e close to the background level of detection)
Answer
  • True
  • False

Question 83

Question
[blank_start]Benjamin[blank_end]-[blank_start]Hochberg[blank_end] [blank_start]FDR[blank_end] is the most common multiple testing correction used in microarray, RNA-seq and proteomics experiments
Answer
  • Benjamin
  • Hochberg
  • FDR

Question 84

Question
Benjamin-Hochberg FDR modifies [blank_start]P[blank_end]-values
Answer
  • P

Question 85

Question
Which of the following are not advantages for RNA-seq experiments over microarrays?
Answer
  • can search for unknown genes
  • can detect very scarce transcripts
  • lower technical variation
  • lower background noise
  • can sequence whole proteome

Question 86

Question
[blank_start]Poly[blank_end]-[blank_start]A[blank_end] [blank_start]selection[blank_end] gets rid of uninteresting, abundant RNA such as rRNA and haemoglobin RNA in blood samples in preparation for RNA-seq experiment
Answer
  • Poly
  • A
  • selection

Question 87

Question
RNA-sequencing relies on reverse transcription
Answer
  • True
  • False

Question 88

Question
RNA-sequencing experiments are quantifiable - the sequencing reads in the library are proportional to the abundance of RNA
Answer
  • True
  • False

Question 89

Question
RPKM and FPKM are examples of [blank_start]normalisation[blank_end] tools used following an RNA-sequencing experiment
Answer
  • normalisation

Question 90

Question
T-tests can be used to analyse microarray and RNA-seq data as both are continuous
Answer
  • True
  • False

Question 91

Question
microarrays can be used to discover novel transcripts
Answer
  • True
  • False

Question 92

Question
transcriptomics is used instead of proteomics as the transcript level always correlates to the protein abundance
Answer
  • True
  • False

Question 93

Question
the two main approaches in expression proteomics experiments are [blank_start]bottom[blank_end] up and [blank_start]top[blank_end] down experiments
Answer
  • bottom
  • top

Question 94

Question
Which of the following are experimental strategies used in proteomics?
Answer
  • liquid chromatography tandem MS
  • 2DGE
  • Microarrays
  • RNA-sequencing

Question 95

Question
Which of the following are disadvantages of 2DGE?
Answer
  • expensive
  • time-consuming
  • limited sensitivity
  • limited resolution
  • low reproducibility

Question 96

Question
[blank_start]DIGE[blank_end] is a variation of 2DGE whereby multiple samples are ran on one gel but are differentially labelled to eliminate running difference between gels
Answer
  • DIGE

Question 97

Question
Technical variation is higher in microarrays and RNA-seq than 2DGE and liquid chromatography tandem MS
Answer
  • True
  • False

Question 98

Question
in 2DGE, proteins are separated based first on [blank_start]charge[blank_end] then on [blank_start]size[blank_end]
Answer
  • charge
  • size

Question 99

Question
progenesis is a software used in [blank_start]2DGE[blank_end] experiments
Answer
  • 2DGE
  • microarray
  • RNA-seq
  • HPLC

Question 100

Question
[blank_start]peptide[blank_end]-[blank_start]mass[blank_end] [blank_start]fingerprinting[blank_end] is used to identify which proteins are contained within spots on a gel from a 2DGE experiment
Answer
  • peptide
  • mass
  • fingerprinting

Question 101

Question
2DGE can be used to identify membrane proteins
Answer
  • True
  • False

Question 102

Question
2DGE cannot be used to show post-translational modifications
Answer
  • True
  • False

Question 103

Question
in a proteomics experiment, proteins are first isolated then digested using an enzyme such as [blank_start]trypsin[blank_end] as it cuts in a predictable ways
Answer
  • trypsin

Question 104

Question
in a peptide-mass fingerprinting experiment, resulting peak-lists can be the same for very similar proteins
Answer
  • True
  • False

Question 105

Question
in tandem MS, when fragments are introduced they are broken up by argon gas, which preferentially breaks peptide bonds
Answer
  • True
  • False

Question 106

Question
Which of the following databases of hypothetical spectra is used to identify peptides from an MS experiment?
Answer
  • Genescan
  • InterPro
  • MASCOT
  • BLOCKS
  • PRINTS
  • iTRAQ

Question 107

Question
the intensity of peaks in MS can be used to quantify proteins
Answer
  • True
  • False

Question 108

Question
[blank_start]hydrophobicity[blank_end] is the main driving force of protein folding process
Answer
  • hydrophobicity

Question 109

Question
secondary structure refers to global interactions within a protein
Answer
  • True
  • False

Question 110

Question
[blank_start]alpha[blank_end] helix, [blank_start]beta[blank_end] sheet and [blank_start]coil[blank_end] are the 3 secondary structure states
Answer
  • coil
  • alpha
  • beta

Question 111

Question
protein [blank_start]domains[blank_end] are subunits within a protein with quasi-independent folding stability
Answer
  • domains

Question 112

Question
the [blank_start]quaternary[blank_end] structure refers to proteins formed from several subunits or monomers
Answer
  • quaternary

Question 113

Question
protein structures solved by NMR or crystallography are saved as [blank_start]PBD[blank_end] files
Answer
  • PBD

Question 114

Question
a [blank_start]Ramachandran[blank_end] [blank_start]plot[blank_end] visualises and clusters residues of an amino acid sequence based on psi and phi angles of the residue backbone
Answer
  • Ramachandran
  • plot

Question 115

Question
CATH, SCOP and FSSP/DDD are all examples of what?
Answer
  • tertiary structure classification methods
  • protein structure prediction assessment
  • databases containing sequence information
  • protein data banks

Question 116

Question
the levels of hierarchy in the CATH system to catalogue proteins are ordered from bottom to top as follows: 1. [blank_start]class[blank_end] 2. [blank_start]architecture[blank_end] 3. [blank_start]fold[blank_end] 4. [blank_start]superfamily[blank_end] 5. [blank_start]domain[blank_end]
Answer
  • class
  • domain
  • architecture
  • superfamily
  • fold
  • architecture
  • class
  • domain
  • fold
  • superfamily
  • fold
  • domain
  • class
  • architecture
  • superfamily
  • superfamily
  • architecture
  • domain
  • class
  • fold
  • domain
  • class
  • architecture
  • fold
  • superfamily

Question 117

Question
mainly alpha and mainly beta are examples of CATH folds
Answer
  • True
  • False

Question 118

Question
3D protein structure prediction is treated as a machine learning problem
Answer
  • True
  • False

Question 119

Question
machine learning in the context of protein structure prediction aims to minimise the energy function
Answer
  • True
  • False

Question 120

Question
Dynamic programming is an optimisation method
Answer
  • True
  • False

Question 121

Question
Which of the following are types of machine learning?
Answer
  • Hidden markov models
  • artificial neural networks
  • rule learning
  • position specific scoring
  • multiple testing correction

Question 122

Question
a [blank_start]PSSM[blank_end] is similar to a substitution matrix but specifically tailored to the sequence being aligned
Answer
  • PSSM

Question 123

Question
[blank_start]PSIPRED[blank_end] is the most popular secondary structure prediction software
Answer
  • PSIPRED

Question 124

Question
PSIPRED uses hidden markov models
Answer
  • True
  • False

Question 125

Question
[blank_start]contact[blank_end] [blank_start]number[blank_end] is the number of connections a residue in a protein has
Answer
  • contact
  • number

Question 126

Question
[blank_start]solvent[blank_end] [blank_start]accessibility[blank_end] is the amount of surface exposed of each residue
Answer
  • solvent
  • accessibility

Question 127

Question
which of the following are the broad approaches for 3D PSP?
Answer
  • De novo
  • Ab initio
  • template-based
  • machine learning

Question 128

Question
which 3 ways can a template by identified for 3D PSP?
Answer
  • homology modelling
  • profile-base methods
  • machine learning
  • threading
  • ab initio modelling

Question 129

Question
Fold recognition is used to identify a template with high structural similarity but low sequence identity with the target protein, when homology modelling is not an option
Answer
  • True
  • False

Question 130

Question
in 3D PSP, profile-based methods make profiles for residues in a sequence based on...
Answer
  • secondary structure
  • hydrophobicity
  • acidity
  • solvent accessibility
  • tertiary structure

Question 131

Question
in 3D PSP, fragment assembly combines [blank_start]homology[blank_end] [blank_start]modelling[blank_end] with [blank_start]ab[blank_end] [blank_start]initio[blank_end] methods
Answer
  • homology
  • modelling
  • ab
  • initio

Question 132

Question
in fragment assembly, [blank_start]decoys[blank_end] are candidate structure generated from all the possible combinations of fragments. They energy minimisation process is applied to them and they are clustered. The final models are selected from the centre of this cluster,
Answer
  • decoys

Question 133

Question
I-Tasser is a [blank_start]pipeline[blank_end] used for protein structure prediction
Answer
  • pipeline

Question 134

Question
a network is a graph consisting of a series of [blank_start]nodes[blank_end] connect by [blank_start]edges[blank_end]
Answer
  • nodes
  • edges

Question 135

Question
in a biological network, genes, proteins and cell types can be depicted as [blank_start]nodes[blank_end]
Answer
  • nodes

Question 136

Question
in a network, sink nodes have high in degree and sources have a high out degree
Answer
  • True
  • False

Question 137

Question
Which of the following is not a type of degree distribution in a network?
Answer
  • constant
  • scale-free
  • random
  • betweenness

Question 138

Question
In a network, the distance can be defined by Pajek or Watts
Answer
  • True
  • False

Question 139

Question
The longest shortest path between all pairs of nodes is...
Answer
  • Pajeks diameter
  • Pajeks distance
  • Watts diameter
  • Watts distance

Question 140

Question
the [blank_start]density[blank_end] is defined by the number of edges as a fraction of the number of possible edges
Answer
  • density

Question 141

Question
Which of the following are measures of centrality of a network?
Answer
  • degree
  • betweenness
  • closeness
  • distance
  • diameter

Question 142

Question
The betweenness centrality is a fraction of the shortest paths of the network for which a certain node is a member of
Answer
  • True
  • False

Question 143

Question
[blank_start]closeness[blank_end] [blank_start]centrality[blank_end] rewards nodes from which within a few edges, any node can be accessed
Answer
  • closeness
  • centrality

Question 144

Question
a random Boolean network is undirected
Answer
  • True
  • False

Question 145

Question
A random Boolean network can be used to study dynamic processes such as gene expression
Answer
  • True
  • False

Question 146

Question
an [blank_start]integrated[blank_end] network uses data from high-quality databases such as BioGrid as well as our own experimental data
Answer
  • integrated

Question 147

Question
Gene co-expression networks are built using [blank_start]guilt[blank_end] by [blank_start]association[blank_end]
Answer
  • guilt
  • association

Question 148

Question
In gene co-expression networks, similarity in expression across samples is usually computed by
Answer
  • pearson's correlation
  • principle component analysis
  • guilt-by-association
  • force

Question 149

Question
A gene co-prediction network relies on a set of rules and an edge connects genes that co-predict with high frequency
Answer
  • True
  • False

Question 150

Question
PathExpand and TopoGSA are examples of network [blank_start]refinement[blank_end] packages
Answer
  • refinement

Question 151

Question
force, arc, circular and hive are all examples of network [blank_start]layout[blank_end]
Answer
  • layout

Question 152

Question
An Arc network is more scalable than a Hive network
Answer
  • True
  • False

Question 153

Question
community detection is also known as [blank_start]clustering[blank_end]
Answer
  • clustering

Question 154

Question
[blank_start]clustering[blank_end] identifies sub-parts of a network with many connections and often reflect meaningful modules within the network organisation i.e cellular machinery or biological processes
Answer
  • clustering

Question 155

Question
[blank_start]ontologies[blank_end] represent relationships in a computationally amenable way by providing controlled vocabulary of terms
Answer
  • ontologies

Question 156

Question
Which of the following are ontologies used by GO to describe the associations of gene products
Answer
  • biological processes
  • cellular components
  • 3D structure
  • interaction partners
  • molecular functions

Question 157

Question
there are [blank_start]20[blank_end] amino acids used in biological systems
Answer
  • 20

Question 158

Question
Which of the following is not commonly used to assess sequencing methods?
Answer
  • read length
  • throughput
  • cost per base
  • cost of the machine
  • sample size

Question 159

Question
Which of the following is not a database combined in the INSDC major collection point for sequencing data?
Answer
  • EMBL-EBI
  • NCBI
  • NIG
  • GenBank

Question 160

Question
Sanger, 454, ion torrent and ilumina sequencing all sequence by [blank_start]synthesis[blank_end]
Answer
  • synthesis

Question 161

Question
Third generation sequencing involves a PCR step
Answer
  • True
  • False

Question 162

Question
the current gold-standard for shotgun sequencing assembly is a [blank_start]100[blank_end]-fold coverage
Answer
  • 100

Question 163

Question
Which of the following is not a reason for making sequence assembly difficult?
Answer
  • biased sequence composition
  • homopolymers
  • repeats
  • long reads

Question 164

Question
coverage assumes that DNA is randomly fragmented and all DNA is able to be sequenced.
Answer
  • True
  • False

Question 165

Question
the coverage equation often underestimates the number of reads necessary
Answer
  • True
  • False

Question 166

Question
silent mutations usually occur in the [blank_start]3rd[blank_end] base of a [blank_start]codon[blank_end]
Answer
  • 3rd
  • codon

Question 167

Question
[blank_start]xenologous[blank_end] genes are those which are homologous and have been gained via horizontal gene transfer
Answer
  • xenologous

Question 168

Question
in sequence alignments a [blank_start]:[blank_end] represents a perfect match, a [blank_start].[blank_end] represents a similar AA and a blank space represents a larger AA change
Answer
  • :
  • .

Question 169

Question
Heuristic alignment methods are better when computational power is not a problem or for a small number of sequences
Answer
  • True
  • False

Question 170

Question
in a BLAST search, the number of hits one can expect to see by chance when searching a database of a particular size is defined by the [blank_start]E[blank_end]-[blank_start]value[blank_end]
Answer
  • E
  • value

Question 171

Question
in a MSA, the alignment table can be summarised in a single line, a pseudo sequence called the [blank_start]consensus[blank_end]
Answer
  • consensus

Question 172

Question
A MSA algorithm which starts with a complete MSA, makes changes, computes score, keeps the MSA if the score is better then repeats is known as an [blank_start]iterative[blank_end] method
Answer
  • iterative

Question 173

Question
In a progression MSA, the original mapping can be changed
Answer
  • True
  • False

Question 174

Question
progressive multiple sequence alignment strategies use pairwise alignments
Answer
  • True
  • False

Question 175

Question
the muscle MSA alignment method uses the [blank_start]kimura[blank_end] [blank_start]distance[blank_end] matrix to make a global alignment during the improved progressive alignment
Answer
  • kimura
  • distance

Question 176

Question
muscle uses WPGMA to make alignments
Answer
  • True
  • False

Question 177

Question
a [blank_start]profile[blank_end] can be incorporated into MSA and PSP algorithms to give better results
Answer
  • profile

Question 178

Question
PSI-BLAST uses a position-specific scoring matrix
Answer
  • True
  • False

Question 179

Question
UPGMA can be fitted with an evolutionary model
Answer
  • True
  • False

Question 180

Question
microarrays assay gene expression by quantification of mRNA using hybridisation
Answer
  • True
  • False

Question 181

Question
[blank_start]quantile[blank_end] normalisation is a method of normalisation which ranks data, then takes the median value for each rank and replace the original values with the ranked averages
Answer
  • quantile

Question 182

Question
principle component analysis reduces multi-dimensional data down to [blank_start]2[blank_end] dimensions
Answer
  • 2

Question 183

Question
when analysing microarray data, multiple testing correction controls for the error rate due to false positives being produced by multiple T-tests
Answer
  • True
  • False

Question 184

Question
which of the following does not encompass the same methods between microarrays and RNA-seq?
Answer
  • normalisation
  • quality control
  • statistical analysis

Question 185

Question
when analysing data from an RNA-seq experiment, DE-seq assumes a [blank_start]negative[blank_end] [blank_start]binomial[blank_end] distribution
Answer
  • negative
  • binomial

Question 186

Question
organisms have 1 genome and 1 proteome
Answer
  • True
  • False

Question 187

Question
in 2DGE, there is a pH gradient running left to right. Where a protein is positioned depends on its [blank_start]isoelectric[blank_end] [blank_start]point[blank_end]
Answer
  • isoelectric
  • point

Question 188

Question
in 2DGE, it is valid to compare spots between gels if the spot is absent on one of the gels
Answer
  • True
  • False

Question 189

Question
Sensitivity is good in 2DGE as the dye is linearly incorporated
Answer
  • True
  • False

Question 190

Question
LC-MS can be multidimensional, separating proteins based on more than 2 physiochemical properties
Answer
  • True
  • False

Question 191

Question
iTRAQ is used to label samples in order to quantify them. Tags are made up of an [blank_start]ester[blank_end] group to tag to the protein, a [blank_start]reporter[blank_end] of varying sizes and a [blank_start]balancer[blank_end] to balance the mass
Answer
  • ester
  • reporter
  • balancer

Question 192

Question
when using iTRAQ to quantify proteins during LC-MS, the balancer moiety is measured - when there is a more balancer moiety, there is a higher peak and therefore more peptide.
Answer
  • True
  • False

Question 193

Question
iTRAQ is a relative quantification method in LC-MS
Answer
  • True
  • False

Question 194

Question
data from LC-MS experiments have been locked in [blank_start]proprietary[blank_end] [blank_start]boxes[blank_end] up until recently, meaning that specialist software was required to view and analyse data depending on the technology used.
Answer
  • proprietary
  • boxes

Question 195

Question
spot profiles for LC-MS data can be clustered [blank_start]statistically[blank_end] based on how similar their expression profiles are or [blank_start]functionally[blank_end] based on how similar their function are
Answer
  • statistically
  • functionally

Question 196

Question
the function of a protein depends on its [blank_start]structure[blank_end]
Answer
  • structure

Question 197

Question
a beta hairpin is an example of a [blank_start]supersecondary[blank_end] structure
Answer
  • supersecondary
  • secondary
  • tertiary
  • CATH
  • primary
  • domain

Question 198

Question
which of the following is not an example of a structural property of an individual residue that can be predicted
Answer
  • supersecondary structure
  • secondary structure
  • solvent accessibility
  • contact number
  • whether it is exposed on the surface

Question 199

Question
predicting structural aspects of protein residues is generally treated as an optimisation problem
Answer
  • True
  • False

Question 200

Question
[blank_start]scaffolding[blank_end] is a technique used to link together non-contiguous series of genomic DNA
Answer
  • scaffolding
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