20590946
Descrição
Quiz por lauren beck, atualizado more than 1 year ago
|
Criado por lauren beck
mais de 4 anos atrás
|
|
Questão 1
Questão
Which of the following are sequence elements that algorithms can exploit to search for genes in a prokaryotic genome?
Responda
-
TFIIB recognition element
-
TATA box at -10
-
ATG start codon
-
STOP codon
-
downstream core promoter element at +30
-
initiator element around transcription start site
Questão 2
Questão
[blank_start]Sanger sequencing[blank_end] is an example of a first generation sequencing technology
Responda
-
Sanger sequencing
Questão 3
Questão
Sanger sequencing has been automated by fluorescent labelling
Responda
- True
- False
Questão 4
Questão
Which of the following are advantages of sanger sequencing?
Responda
-
high accuracy
-
good for short sequences
-
high throughput
-
cheap
-
long read length
Questão 5
Questão
select the technologies that are second generation sequencing methods
Responda
-
Sanger
-
454 pyrosequencing
-
Ilumina
-
Ion torrent
-
nanopore
-
PacBio
Questão 6
Questão
Which of the following are limitations of 454 pyrosequencing?
Responda
-
slow sample preparation
-
lower throughput than sanger
-
shorter read lengths than sanger
-
homopolymer errors
Questão 7
Questão
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
Responda
- True
- False
Questão 8
Questão
454 pyrosequencing and ion torrent use solid-phase bridge PCR
Responda
- True
- False
Questão 9
Questão
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]
Responda
-
pH
-
light
Questão 10
Questão
What are the advantages of third generation sequencing technologies?
Responda
-
High accuracy
-
high throughput
-
longer read length
-
Low cost
-
minimal sample preparation
Questão 11
Questão
[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
Responda
-
human
-
genome
-
project
-
encode
-
1000
-
genomes
-
project
Questão 12
Questão
[blank_start]shotgun[blank_end] [blank_start]sequencing[blank_end] is the most common sequencing approach for whole genomes
Responda
-
shotgun
-
sequencing
Questão 13
Questão
a [blank_start]contig[blank_end] is a set of overlapping DNA fragments that together represent a consensus region of DNA
Responda
-
contig
-
scaffold
-
read
-
coverage
Questão 14
Questão
the de bruijn graph method is a greedy method of assembly
Responda
- True
- False
Questão 15
Questão
[blank_start]k[blank_end] is the parameter used in the de bruijn graph assembly algorithm
Responda
-
k
Questão 16
Questão
sequence assembly can be...
Responda
-
ab initio
-
de novo
-
read mapping
Questão 17
Questão
Which of the following are de bruijn graph sequence assemblers?
Responda
-
Celera
-
GigAssembler
-
Velvet
-
SPAdes
Questão 18
Questão
Genomes always need to be finished
Responda
- True
- False
Questão 19
Questão
hybrid sequencing is an effective way of closing gaps in genome assembly as different technologies are biased in sequencing in different ways
Responda
- True
- False
Questão 20
Questão
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
Responda
-
reads
-
coverage
-
genome length
-
read length
-
coverage
-
reads
-
genome length
-
read length
Questão 21
Questão
Which of the following are examples of challenges faced during sequence assembly?
Responda
-
sequencing errors
-
shotgun fragmenting is not random
-
repeated regions
-
computational power
-
throughput
-
cost
Questão 22
Questão
Why can't BLAST be used for short read mapping to assemble our reads using a reference genome?
Responda
-
it costs too much and is highly inaccurate
-
it is not compatible
-
it takes too long and is not good at finding close matches
Questão 23
Questão
when might short-read mapping be beneficial to use?
Responda
-
for RNA-sequencing experiments
-
for chipping experiments
-
to assemble a whole genome
-
to find open reading frames
Questão 24
Questão
[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
Responda
-
Burrows
-
wheeler
Questão 25
Questão
We always need to assemble the genome in metagenomics experiments
Responda
- True
- False
Questão 26
Questão
raw sequencing data from sequencing experiments are saved in the sequence read archive
Responda
- True
- False
Questão 27
Questão
annotated sequence data from sequencing experiments are saved in GenBank and EMBL
Responda
- True
- False
Questão 28
Questão
Which of the following are legitimate methods of assessing a sequence assembly?
Responda
-
the N50 statistic
-
principle component analysis
-
average gap size
-
average number of gaps per scaffold
-
coverage
-
hierarchical clusterin
Questão 29
Questão
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
Responda
- True
- False
Questão 30
Questão
sequence annotation involves identifying...
Responda
-
read lengths
-
coverage
-
CDSs
-
promoters
-
ribosome binding sites
-
introns
-
exons
Questão 31
Questão
gene prediction involves finding UTRs and alternative splice isoforms
Responda
- True
- False
Questão 32
Questão
what are the 2 major approaches for gene finding?
Responda
-
ab initio
-
comparative proteomics
-
comparative genomics
-
de novo
Questão 33
Questão
ab initio gene finding approaches are more accurate for eukaryotes than prokaryotes
Responda
- True
- False
Questão 34
Questão
the gene finding tools Glimmer and GeneScan use [blank_start]hidden[blank_end] [blank_start]markov[blank_end] models
Responda
-
hidden
-
markov
Questão 35
Questão
which of the following make eukaryotic gene finding more difficult than prokaryotic gene finding?
Responda
-
high number of repeats
-
introns
-
exons
-
highly compact
-
alternative splicing
Questão 36
Questão
What measures can be used to assess gene prediction?
Responda
-
sensitivity
-
specificity
-
accuracy
-
N50 statistic
Questão 37
Questão
There is a trade-off when it comes to the specificity and sensitivity of gene prediction tools
Responda
- True
- False
Questão 38
Questão
[blank_start]prokka[blank_end] is a genome annotation pipeline good for prokaryotes and small eukaryotes
Responda
-
prokka
-
genescan
-
glimmer
-
genie
Questão 39
Questão
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]
Responda
-
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
Questão 40
Questão
silent, missense and nonsense are all types of [blank_start]point[blank_end] mutation
Responda
-
point
Questão 41
Questão
nonsense mutations can be conservative or non-conservative (similar AA or not)
Responda
- True
- False
Questão 42
Questão
introns, intergenic regions and pseudogenes are highly conserved and intolerant to change
Responda
- True
- False
Questão 43
Questão
Gene duplicates experience relaxed evolutionary constraints
Responda
- True
- False
Questão 44
Questão
when does gene duplication occur in bacteria?
Responda
-
in response to favourable conditions
-
in response to stress
-
in response to an internal stimulus
-
linearly over evolutionary time
Questão 45
Questão
[blank_start]duplication[blank_end] is an essential mutation for evolutionary change to occur in eukaryotes
Responda
-
duplication
-
point mutation
-
inversion
-
insertion
-
deletion
Questão 46
Questão
gene duplication can lead to [blank_start]nonfunctionalisation[blank_end] [blank_start]neofunctionalisation[blank_end] or [blank_start]subfunctionalisation[blank_end]
Responda
-
nonfunctionalisation
-
neofunctionalisation
-
subfunctionalisation
Questão 47
Questão
which of the following are sources of variation in prokaryotes?
Responda
-
lateral gene transfer
-
endosymbiosis
-
mutations
Questão 48
Questão
genes that share a common ancestor are said to be what?
Responda
-
homologs
-
paralogs
-
orthologs
-
xenologs
Questão 49
Questão
genes that have diverged as a result of speciation are said to be what?
Responda
-
homologs
-
orthologs
-
paralogs
-
xenologs
Questão 50
Questão
genes within the same genome created as a result of gene duplication are said to be what?
Responda
-
homologs
-
orthologs
-
paralogs
-
xenologs
Questão 51
Questão
homology is a measure of similarity
Responda
- True
- False
Questão 52
Questão
which of the following are simplistic measure of similarity when it comes to measuring sequence similarity?
Responda
-
hamming distance
-
sequence identity
-
levenshtein distance
-
PAM250
-
BLOSUM62
Questão 53
Questão
what kind of mutations are more common?
Responda
-
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
Questão 54
Questão
PAM and BLOSUM are example of [blank_start]substitution[blank_end] [blank_start]matrices[blank_end]
Responda
-
substitution
-
matrices
Questão 55
Questão
1 PAM is 1% similarity
Responda
- True
- False
Questão 56
Questão
PAM is better for [blank_start]global[blank_end] alignments whilst BLOSUM is better for [blank_start]local[blank_end] alignments
Responda
-
global
-
local
Questão 57
Questão
BLOSUM matrices are derived from the [blank_start]BLOCKS[blank_end] database
Responda
-
BLOCKS
Questão 58
Questão
A higher PAM matrix will find weaker, longer alignments and a BLOSUM matrix with a higher number are better for similar sequences
Responda
- True
- False
Questão 59
Questão
A local alignment tries to align all the residues in a sequence
Responda
- True
- False
Questão 60
Questão
Dynamic programming is used for [blank_start]exact[blank_end] alignment methods
Responda
-
exact
Questão 61
Questão
Needleman-Wunsch is a [blank_start]global[blank_end] alignment algorithm
Responda
-
global
Questão 62
Questão
Smith-waterman is a local alignment algorithm
Responda
- True
- False
Questão 63
Questão
The trajectory refers to the traceback arrows in a trajectory table
Responda
- True
- False
Questão 64
Questão
BLAST and FASTA are examples of [blank_start]heuristic[blank_end] alignment methods
Responda
-
heuristic
Questão 65
Questão
Exact alignment methods are not guaranteed to find an optimal solution
Responda
- True
- False
Questão 66
Questão
K-tuple alignment methods are a family of approximate alignment methods, and BLAST is part of the family
Responda
- True
- False
Questão 67
Questão
a [blank_start]heuristic[blank_end] approach is taken with multiple sequence alignment because an exact approach has complexity O(L^N)
Responda
-
heuristic
Questão 68
Questão
progressive, iterative and statistical are all approaches used for [blank_start]MSA[blank_end]
Responda
-
MSA
Questão 69
Questão
Which of the following are examples of progressive alignment algorithms?
Responda
-
T-coffee
-
Clustal omega
-
Clustal W
-
Muscle
Questão 70
Questão
Which of the following algorithms takes a hybrid approach for multiple sequence alignment?
Responda
-
T-coffee
-
Muscle
-
Clustal omega
-
Clustal W
Questão 71
Questão
A [blank_start]motif[blank_end] is part of a protein sequence associated with a particular biological function
Responda
-
motif
Questão 72
Questão
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
Responda
-
profile
-
pattern
-
pattern
-
profile
Questão 73
Questão
Which of the following databases describe motifs in terms of pattern and profile?
Responda
-
Pfam
-
PROSITE
-
InterPro
-
GeneBank
-
EMBL
-
BLOCKS
Questão 74
Questão
PSI-BLAST is more powerful than BLAST for picking up distant relationships between sequences
Responda
- True
- False
Questão 75
Questão
in phylogenetics, masking an alignment involved looking for regions or conservation and removing data that does not appear homologous
Responda
- True
- False
Questão 76
Questão
Which of the following are examples of distance-based tree building methods?
Responda
-
Maximum likelihood
-
Maximum parsimony
-
UPGMA
-
WPGMA
-
Bayesian inference
Questão 77
Questão
[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
Responda
-
Bootstrap
-
values
Questão 78
Questão
[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
Responda
-
WPGMA
Questão 79
Questão
microarrays and RNA-sequencing are examples of what kind of experiments?
Responda
-
genomics
-
transcriptomics
-
proteomics
-
phylogenetics
Questão 80
Questão
[blank_start]normalisation[blank_end] aims to remove technical variation existing in microarray experiments
Responda
-
normalisation
Questão 81
Questão
Which of the following are methods for quality control to remove outliers from microarray experiments?
Responda
-
N50 statistic
-
hierarchical clustering
-
normalisation
-
principle component analysis
-
probeset QC
-
multiple testing correction
Questão 82
Questão
following a microarray experiment, probeset QC removes noise and uninformative data points (i.e close to the background level of detection)
Responda
- True
- False
Questão 83
Questão
[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
Responda
-
Benjamin
-
Hochberg
-
FDR
Questão 84
Questão
Benjamin-Hochberg FDR modifies [blank_start]P[blank_end]-values
Responda
-
P
Questão 85
Questão
Which of the following are not advantages for RNA-seq experiments over microarrays?
Responda
-
can search for unknown genes
-
can detect very scarce transcripts
-
lower technical variation
-
lower background noise
-
can sequence whole proteome
Questão 86
Questão
[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
Responda
-
Poly
-
A
-
selection
Questão 87
Questão
RNA-sequencing relies on reverse transcription
Responda
- True
- False
Questão 88
Questão
RNA-sequencing experiments are quantifiable - the sequencing reads in the library are proportional to the abundance of RNA
Responda
- True
- False
Questão 89
Questão
RPKM and FPKM are examples of [blank_start]normalisation[blank_end] tools used following an RNA-sequencing experiment
Responda
-
normalisation
Questão 90
Questão
T-tests can be used to analyse microarray and RNA-seq data as both are continuous
Responda
- True
- False
Questão 91
Questão
microarrays can be used to discover novel transcripts
Responda
- True
- False
Questão 92
Questão
transcriptomics is used instead of proteomics as the transcript level always correlates to the protein abundance
Responda
- True
- False
Questão 93
Questão
the two main approaches in expression proteomics experiments are [blank_start]bottom[blank_end] up and [blank_start]top[blank_end] down experiments
Responda
-
bottom
-
top
Questão 94
Questão
Which of the following are experimental strategies used in proteomics?
Responda
-
liquid chromatography tandem MS
-
2DGE
-
Microarrays
-
RNA-sequencing
Questão 95
Questão
Which of the following are disadvantages of 2DGE?
Responda
-
expensive
-
time-consuming
-
limited sensitivity
-
limited resolution
-
low reproducibility
Questão 96
Questão
[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
Responda
-
DIGE
Questão 97
Questão
Technical variation is higher in microarrays and RNA-seq than 2DGE and liquid chromatography tandem MS
Responda
- True
- False
Questão 98
Questão
in 2DGE, proteins are separated based first on [blank_start]charge[blank_end] then on [blank_start]size[blank_end]
Responda
-
charge
-
size
Questão 99
Questão
progenesis is a software used in [blank_start]2DGE[blank_end] experiments
Responda
-
2DGE
-
microarray
-
RNA-seq
-
HPLC
Questão 100
Questão
[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
Responda
-
peptide
-
mass
-
fingerprinting
Questão 101
Questão
2DGE can be used to identify membrane proteins
Responda
- True
- False
Questão 102
Questão
2DGE cannot be used to show post-translational modifications
Responda
- True
- False
Questão 103
Questão
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
Responda
-
trypsin
Questão 104
Questão
in a peptide-mass fingerprinting experiment, resulting peak-lists can be the same for very similar proteins
Responda
- True
- False
Questão 105
Questão
in tandem MS, when fragments are introduced they are broken up by argon gas, which preferentially breaks peptide bonds
Responda
- True
- False
Questão 106
Questão
Which of the following databases of hypothetical spectra is used to identify peptides from an MS experiment?
Responda
-
Genescan
-
InterPro
-
MASCOT
-
BLOCKS
-
PRINTS
-
iTRAQ
Questão 107
Questão
the intensity of peaks in MS can be used to quantify proteins
Responda
- True
- False
Questão 108
Questão
[blank_start]hydrophobicity[blank_end] is the main driving force of protein folding process
Responda
-
hydrophobicity
Questão 109
Questão
secondary structure refers to global interactions within a protein
Responda
- True
- False
Questão 110
Questão
[blank_start]alpha[blank_end] helix, [blank_start]beta[blank_end] sheet and [blank_start]coil[blank_end] are the 3 secondary structure states
Responda
-
coil
-
alpha
-
beta
Questão 111
Questão
protein [blank_start]domains[blank_end] are subunits within a protein with quasi-independent folding stability
Responda
-
domains
Questão 112
Questão
the [blank_start]quaternary[blank_end] structure refers to proteins formed from several subunits or monomers
Responda
-
quaternary
Questão 113
Questão
protein structures solved by NMR or crystallography are saved as [blank_start]PBD[blank_end] files
Responda
-
PBD
Questão 114
Questão
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
Responda
-
Ramachandran
-
plot
Questão 115
Questão
CATH, SCOP and FSSP/DDD are all examples of what?
Responda
-
tertiary structure classification methods
-
protein structure prediction assessment
-
databases containing sequence information
-
protein data banks
Questão 116
Questão
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]
Responda
-
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
Questão 117
Questão
mainly alpha and mainly beta are examples of CATH folds
Responda
- True
- False
Questão 118
Questão
3D protein structure prediction is treated as a machine learning problem
Responda
- True
- False
Questão 119
Questão
machine learning in the context of protein structure prediction aims to minimise the energy function
Responda
- True
- False
Questão 120
Questão
Dynamic programming is an optimisation method
Responda
- True
- False
Questão 121
Questão
Which of the following are types of machine learning?
Responda
-
Hidden markov models
-
artificial neural networks
-
rule learning
-
position specific scoring
-
multiple testing correction
Questão 122
Questão
a [blank_start]PSSM[blank_end] is similar to a substitution matrix but specifically tailored to the sequence being aligned
Responda
-
PSSM
Questão 123
Questão
[blank_start]PSIPRED[blank_end] is the most popular secondary structure prediction software
Responda
-
PSIPRED
Questão 124
Questão
PSIPRED uses hidden markov models
Responda
- True
- False
Questão 125
Questão
[blank_start]contact[blank_end] [blank_start]number[blank_end] is the number of connections a residue in a protein has
Responda
-
contact
-
number
Questão 126
Questão
[blank_start]solvent[blank_end] [blank_start]accessibility[blank_end] is the amount of surface exposed of each residue
Responda
-
solvent
-
accessibility
Questão 127
Questão
which of the following are the broad approaches for 3D PSP?
Responda
-
De novo
-
Ab initio
-
template-based
-
machine learning
Questão 128
Questão
which 3 ways can a template by identified for 3D PSP?
Responda
-
homology modelling
-
profile-base methods
-
machine learning
-
threading
-
ab initio modelling
Questão 129
Questão
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
Responda
- True
- False
Questão 130
Questão
in 3D PSP, profile-based methods make profiles for residues in a sequence based on...
Responda
-
secondary structure
-
hydrophobicity
-
acidity
-
solvent accessibility
-
tertiary structure
Questão 131
Questão
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
Responda
-
homology
-
modelling
-
ab
-
initio
Questão 132
Questão
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,
Responda
-
decoys
Questão 133
Questão
I-Tasser is a [blank_start]pipeline[blank_end] used for protein structure prediction
Responda
-
pipeline
Questão 134
Questão
a network is a graph consisting of a series of [blank_start]nodes[blank_end] connect by [blank_start]edges[blank_end]
Responda
-
nodes
-
edges
Questão 135
Questão
in a biological network, genes, proteins and cell types can be depicted as [blank_start]nodes[blank_end]
Responda
-
nodes
Questão 136
Questão
in a network, sink nodes have high in degree and sources have a high out degree
Responda
- True
- False
Questão 137
Questão
Which of the following is not a type of degree distribution in a network?
Responda
-
constant
-
scale-free
-
random
-
betweenness
Questão 138
Questão
In a network, the distance can be defined by Pajek or Watts
Responda
- True
- False
Questão 139
Questão
The longest shortest path between all pairs of nodes is...
Responda
-
Pajeks diameter
-
Pajeks distance
-
Watts diameter
-
Watts distance
Questão 140
Questão
the [blank_start]density[blank_end] is defined by the number of edges as a fraction of the number of possible edges
Responda
-
density
Questão 141
Questão
Which of the following are measures of centrality of a network?
Responda
-
degree
-
betweenness
-
closeness
-
distance
-
diameter
Questão 142
Questão
The betweenness centrality is a fraction of the shortest paths of the network for which a certain node is a member of
Responda
- True
- False
Questão 143
Questão
[blank_start]closeness[blank_end] [blank_start]centrality[blank_end] rewards nodes from which within a few edges, any node can be accessed
Responda
-
closeness
-
centrality
Questão 144
Questão
a random Boolean network is undirected
Responda
- True
- False
Questão 145
Questão
A random Boolean network can be used to study dynamic processes such as gene expression
Responda
- True
- False
Questão 146
Questão
an [blank_start]integrated[blank_end] network uses data from high-quality databases such as BioGrid as well as our own experimental data
Responda
-
integrated
Questão 147
Questão
Gene co-expression networks are built using [blank_start]guilt[blank_end] by [blank_start]association[blank_end]
Responda
-
guilt
-
association
Questão 148
Questão
In gene co-expression networks, similarity in expression across samples is usually computed by
Responda
-
pearson's correlation
-
principle component analysis
-
guilt-by-association
-
force
Questão 149
Questão
A gene co-prediction network relies on a set of rules and an edge connects genes that co-predict with high frequency
Responda
- True
- False
Questão 150
Questão
PathExpand and TopoGSA are examples of network [blank_start]refinement[blank_end] packages
Responda
-
refinement
Questão 151
Questão
force, arc, circular and hive are all examples of network [blank_start]layout[blank_end]
Responda
-
layout
Questão 152
Questão
An Arc network is more scalable than a Hive network
Responda
- True
- False
Questão 153
Questão
community detection is also known as [blank_start]clustering[blank_end]
Responda
-
clustering
Questão 154
Questão
[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
Responda
-
clustering
Questão 155
Questão
[blank_start]ontologies[blank_end] represent relationships in a computationally amenable way by providing controlled vocabulary of terms
Responda
-
ontologies
Questão 156
Questão
Which of the following are ontologies used by GO to describe the associations of gene products
Responda
-
biological processes
-
cellular components
-
3D structure
-
interaction partners
-
molecular functions
Questão 157
Questão
there are [blank_start]20[blank_end] amino acids used in biological systems
Responda
-
20
Questão 158
Questão
Which of the following is not commonly used to assess sequencing methods?
Responda
-
read length
-
throughput
-
cost per base
-
cost of the machine
-
sample size
Questão 159
Questão
Which of the following is not a database combined in the INSDC major collection point for sequencing data?
Responda
-
EMBL-EBI
-
NCBI
-
NIG
-
GenBank
Questão 160
Questão
Sanger, 454, ion torrent and ilumina sequencing all sequence by [blank_start]synthesis[blank_end]
Responda
-
synthesis
Questão 161
Questão
Third generation sequencing involves a PCR step
Responda
- True
- False
Questão 162
Questão
the current gold-standard for shotgun sequencing assembly is a [blank_start]100[blank_end]-fold coverage
Responda
-
100
Questão 163
Questão
Which of the following is not a reason for making sequence assembly difficult?
Responda
-
biased sequence composition
-
homopolymers
-
repeats
-
long reads
Questão 164
Questão
coverage assumes that DNA is randomly fragmented and all DNA is able to be sequenced.
Responda
- True
- False
Questão 165
Questão
the coverage equation often underestimates the number of reads necessary
Responda
- True
- False
Questão 166
Questão
silent mutations usually occur in the [blank_start]3rd[blank_end] base of a [blank_start]codon[blank_end]
Responda
-
3rd
-
codon
Questão 167
Questão
[blank_start]xenologous[blank_end] genes are those which are homologous and have been gained via horizontal gene transfer
Responda
-
xenologous
Questão 168
Questão
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
Responda
-
:
-
.
Questão 169
Questão
Heuristic alignment methods are better when computational power is not a problem or for a small number of sequences
Responda
- True
- False
Questão 170
Questão
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]
Responda
-
E
-
value
Questão 171
Questão
in a MSA, the alignment table can be summarised in a single line, a pseudo sequence called the [blank_start]consensus[blank_end]
Responda
-
consensus
Questão 172
Questão
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
Responda
-
iterative
Questão 173
Questão
In a progression MSA, the original mapping can be changed
Responda
- True
- False
Questão 174
Questão
progressive multiple sequence alignment strategies use pairwise alignments
Responda
- True
- False
Questão 175
Questão
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
Responda
-
kimura
-
distance
Questão 176
Questão
muscle uses WPGMA to make alignments
Responda
- True
- False
Questão 177
Questão
a [blank_start]profile[blank_end] can be incorporated into MSA and PSP algorithms to give better results
Responda
-
profile
Questão 178
Questão
PSI-BLAST uses a position-specific scoring matrix
Responda
- True
- False
Questão 179
Questão
UPGMA can be fitted with an evolutionary model
Responda
- True
- False
Questão 180
Questão
microarrays assay gene expression by quantification of mRNA using hybridisation
Responda
- True
- False
Questão 181
Questão
[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
Responda
-
quantile
Questão 182
Questão
principle component analysis reduces multi-dimensional data down to [blank_start]2[blank_end] dimensions
Responda
-
2
Questão 183
Questão
when analysing microarray data, multiple testing correction controls for the error rate due to false positives being produced by multiple T-tests
Responda
- True
- False
Questão 184
Questão
which of the following does not encompass the same methods between microarrays and RNA-seq?
Responda
-
normalisation
-
quality control
-
statistical analysis
Questão 185
Questão
when analysing data from an RNA-seq experiment, DE-seq assumes a [blank_start]negative[blank_end] [blank_start]binomial[blank_end] distribution
Responda
-
negative
-
binomial
Questão 186
Questão
organisms have 1 genome and 1 proteome
Responda
- True
- False
Questão 187
Questão
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]
Responda
-
isoelectric
-
point
Questão 188
Questão
in 2DGE, it is valid to compare spots between gels if the spot is absent on one of the gels
Responda
- True
- False
Questão 189
Questão
Sensitivity is good in 2DGE as the dye is linearly incorporated
Responda
- True
- False
Questão 190
Questão
LC-MS can be multidimensional, separating proteins based on more than 2 physiochemical properties
Responda
- True
- False
Questão 191
Questão
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
Responda
-
ester
-
reporter
-
balancer
Questão 192
Questão
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.
Responda
- True
- False
Questão 193
Questão
iTRAQ is a relative quantification method in LC-MS
Responda
- True
- False
Questão 194
Questão
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.
Responda
-
proprietary
-
boxes
Questão 195
Questão
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
Responda
-
statistically
-
functionally
Questão 196
Questão
the function of a protein depends on its [blank_start]structure[blank_end]
Responda
-
structure
Questão 197
Questão
a beta hairpin is an example of a [blank_start]supersecondary[blank_end] structure
Responda
-
supersecondary
-
secondary
-
tertiary
-
CATH
-
primary
-
domain
Questão 198
Questão
which of the following is not an example of a structural property of an individual residue that can be predicted
Responda
-
supersecondary structure
-
secondary structure
-
solvent accessibility
-
contact number
-
whether it is exposed on the surface
Questão 199
Questão
predicting structural aspects of protein residues is generally treated as an optimisation problem
Responda
- True
- False
Questão 200
Questão
[blank_start]scaffolding[blank_end] is a technique used to link together non-contiguous series of genomic DNA
Responda
-
scaffolding
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