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Bioinformatics

Beschreibung

Quiz am Bioinformatics, erstellt von lauren beck am 19/01/2020.
lauren beck
Quiz von lauren beck, aktualisiert more than 1 year ago
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Erstellt von lauren beck vor mehr als 4 Jahre
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Zusammenfassung der Ressource

Frage 1

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

Frage 2

Frage
[blank_start]Sanger sequencing[blank_end] is an example of a first generation sequencing technology
Antworten
  • Sanger sequencing

Frage 3

Frage
Sanger sequencing has been automated by fluorescent labelling
Antworten
  • True
  • False

Frage 4

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

Frage 5

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

Frage 6

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

Frage 7

Frage
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
Antworten
  • True
  • False

Frage 8

Frage
454 pyrosequencing and ion torrent use solid-phase bridge PCR
Antworten
  • True
  • False

Frage 9

Frage
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]
Antworten
  • pH
  • light

Frage 10

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

Frage 11

Frage
[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
Antworten
  • human
  • genome
  • project
  • encode
  • 1000
  • genomes
  • project

Frage 12

Frage
[blank_start]shotgun[blank_end] [blank_start]sequencing[blank_end] is the most common sequencing approach for whole genomes
Antworten
  • shotgun
  • sequencing

Frage 13

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

Frage 14

Frage
the de bruijn graph method is a greedy method of assembly
Antworten
  • True
  • False

Frage 15

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

Frage 16

Frage
sequence assembly can be...
Antworten
  • ab initio
  • de novo
  • read mapping

Frage 17

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

Frage 18

Frage
Genomes always need to be finished
Antworten
  • True
  • False

Frage 19

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

Frage 20

Frage
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
Antworten
  • reads
  • coverage
  • genome length
  • read length
  • coverage
  • reads
  • genome length
  • read length

Frage 21

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

Frage 22

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

Frage 23

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

Frage 24

Frage
[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
Antworten
  • Burrows
  • wheeler

Frage 25

Frage
We always need to assemble the genome in metagenomics experiments
Antworten
  • True
  • False

Frage 26

Frage
raw sequencing data from sequencing experiments are saved in the sequence read archive
Antworten
  • True
  • False

Frage 27

Frage
annotated sequence data from sequencing experiments are saved in GenBank and EMBL
Antworten
  • True
  • False

Frage 28

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

Frage 29

Frage
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
Antworten
  • True
  • False

Frage 30

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

Frage 31

Frage
gene prediction involves finding UTRs and alternative splice isoforms
Antworten
  • True
  • False

Frage 32

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

Frage 33

Frage
ab initio gene finding approaches are more accurate for eukaryotes than prokaryotes
Antworten
  • True
  • False

Frage 34

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

Frage 35

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

Frage 36

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

Frage 37

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

Frage 38

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

Frage 39

Frage
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]
Antworten
  • 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

Frage 40

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

Frage 41

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

Frage 42

Frage
introns, intergenic regions and pseudogenes are highly conserved and intolerant to change
Antworten
  • True
  • False

Frage 43

Frage
Gene duplicates experience relaxed evolutionary constraints
Antworten
  • True
  • False

Frage 44

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

Frage 45

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

Frage 46

Frage
gene duplication can lead to [blank_start]nonfunctionalisation[blank_end] [blank_start]neofunctionalisation[blank_end] or [blank_start]subfunctionalisation[blank_end]
Antworten
  • nonfunctionalisation
  • neofunctionalisation
  • subfunctionalisation

Frage 47

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

Frage 48

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

Frage 49

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

Frage 50

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

Frage 51

Frage
homology is a measure of similarity
Antworten
  • True
  • False

Frage 52

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

Frage 53

Frage
what kind of mutations are more common?
Antworten
  • 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

Frage 54

Frage
PAM and BLOSUM are example of [blank_start]substitution[blank_end] [blank_start]matrices[blank_end]
Antworten
  • substitution
  • matrices

Frage 55

Frage
1 PAM is 1% similarity
Antworten
  • True
  • False

Frage 56

Frage
PAM is better for [blank_start]global[blank_end] alignments whilst BLOSUM is better for [blank_start]local[blank_end] alignments
Antworten
  • global
  • local

Frage 57

Frage
BLOSUM matrices are derived from the [blank_start]BLOCKS[blank_end] database
Antworten
  • BLOCKS

Frage 58

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

Frage 59

Frage
A local alignment tries to align all the residues in a sequence
Antworten
  • True
  • False

Frage 60

Frage
Dynamic programming is used for [blank_start]exact[blank_end] alignment methods
Antworten
  • exact

Frage 61

Frage
Needleman-Wunsch is a [blank_start]global[blank_end] alignment algorithm
Antworten
  • global

Frage 62

Frage
Smith-waterman is a local alignment algorithm
Antworten
  • True
  • False

Frage 63

Frage
The trajectory refers to the traceback arrows in a trajectory table
Antworten
  • True
  • False

Frage 64

Frage
BLAST and FASTA are examples of [blank_start]heuristic[blank_end] alignment methods
Antworten
  • heuristic

Frage 65

Frage
Exact alignment methods are not guaranteed to find an optimal solution
Antworten
  • True
  • False

Frage 66

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

Frage 67

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

Frage 68

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

Frage 69

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

Frage 70

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

Frage 71

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

Frage 72

Frage
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
Antworten
  • profile
  • pattern
  • pattern
  • profile

Frage 73

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

Frage 74

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

Frage 75

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

Frage 76

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

Frage 77

Frage
[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
Antworten
  • Bootstrap
  • values

Frage 78

Frage
[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
Antworten
  • WPGMA

Frage 79

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

Frage 80

Frage
[blank_start]normalisation[blank_end] aims to remove technical variation existing in microarray experiments
Antworten
  • normalisation

Frage 81

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

Frage 82

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

Frage 83

Frage
[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
Antworten
  • Benjamin
  • Hochberg
  • FDR

Frage 84

Frage
Benjamin-Hochberg FDR modifies [blank_start]P[blank_end]-values
Antworten
  • P

Frage 85

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

Frage 86

Frage
[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
Antworten
  • Poly
  • A
  • selection

Frage 87

Frage
RNA-sequencing relies on reverse transcription
Antworten
  • True
  • False

Frage 88

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

Frage 89

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

Frage 90

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

Frage 91

Frage
microarrays can be used to discover novel transcripts
Antworten
  • True
  • False

Frage 92

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

Frage 93

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

Frage 94

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

Frage 95

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

Frage 96

Frage
[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
Antworten
  • DIGE

Frage 97

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

Frage 98

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

Frage 99

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

Frage 100

Frage
[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
Antworten
  • peptide
  • mass
  • fingerprinting

Frage 101

Frage
2DGE can be used to identify membrane proteins
Antworten
  • True
  • False

Frage 102

Frage
2DGE cannot be used to show post-translational modifications
Antworten
  • True
  • False

Frage 103

Frage
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
Antworten
  • trypsin

Frage 104

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

Frage 105

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

Frage 106

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

Frage 107

Frage
the intensity of peaks in MS can be used to quantify proteins
Antworten
  • True
  • False

Frage 108

Frage
[blank_start]hydrophobicity[blank_end] is the main driving force of protein folding process
Antworten
  • hydrophobicity

Frage 109

Frage
secondary structure refers to global interactions within a protein
Antworten
  • True
  • False

Frage 110

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

Frage 111

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

Frage 112

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

Frage 113

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

Frage 114

Frage
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
Antworten
  • Ramachandran
  • plot

Frage 115

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

Frage 116

Frage
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]
Antworten
  • 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

Frage 117

Frage
mainly alpha and mainly beta are examples of CATH folds
Antworten
  • True
  • False

Frage 118

Frage
3D protein structure prediction is treated as a machine learning problem
Antworten
  • True
  • False

Frage 119

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

Frage 120

Frage
Dynamic programming is an optimisation method
Antworten
  • True
  • False

Frage 121

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

Frage 122

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

Frage 123

Frage
[blank_start]PSIPRED[blank_end] is the most popular secondary structure prediction software
Antworten
  • PSIPRED

Frage 124

Frage
PSIPRED uses hidden markov models
Antworten
  • True
  • False

Frage 125

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

Frage 126

Frage
[blank_start]solvent[blank_end] [blank_start]accessibility[blank_end] is the amount of surface exposed of each residue
Antworten
  • solvent
  • accessibility

Frage 127

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

Frage 128

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

Frage 129

Frage
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
Antworten
  • True
  • False

Frage 130

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

Frage 131

Frage
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
Antworten
  • homology
  • modelling
  • ab
  • initio

Frage 132

Frage
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,
Antworten
  • decoys

Frage 133

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

Frage 134

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

Frage 135

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

Frage 136

Frage
in a network, sink nodes have high in degree and sources have a high out degree
Antworten
  • True
  • False

Frage 137

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

Frage 138

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

Frage 139

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

Frage 140

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

Frage 141

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

Frage 142

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

Frage 143

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

Frage 144

Frage
a random Boolean network is undirected
Antworten
  • True
  • False

Frage 145

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

Frage 146

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

Frage 147

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

Frage 148

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

Frage 149

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

Frage 150

Frage
PathExpand and TopoGSA are examples of network [blank_start]refinement[blank_end] packages
Antworten
  • refinement

Frage 151

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

Frage 152

Frage
An Arc network is more scalable than a Hive network
Antworten
  • True
  • False

Frage 153

Frage
community detection is also known as [blank_start]clustering[blank_end]
Antworten
  • clustering

Frage 154

Frage
[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
Antworten
  • clustering

Frage 155

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

Frage 156

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

Frage 157

Frage
there are [blank_start]20[blank_end] amino acids used in biological systems
Antworten
  • 20

Frage 158

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

Frage 159

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

Frage 160

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

Frage 161

Frage
Third generation sequencing involves a PCR step
Antworten
  • True
  • False

Frage 162

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

Frage 163

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

Frage 164

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

Frage 165

Frage
the coverage equation often underestimates the number of reads necessary
Antworten
  • True
  • False

Frage 166

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

Frage 167

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

Frage 168

Frage
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
Antworten
  • :
  • .

Frage 169

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

Frage 170

Frage
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]
Antworten
  • E
  • value

Frage 171

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

Frage 172

Frage
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
Antworten
  • iterative

Frage 173

Frage
In a progression MSA, the original mapping can be changed
Antworten
  • True
  • False

Frage 174

Frage
progressive multiple sequence alignment strategies use pairwise alignments
Antworten
  • True
  • False

Frage 175

Frage
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
Antworten
  • kimura
  • distance

Frage 176

Frage
muscle uses WPGMA to make alignments
Antworten
  • True
  • False

Frage 177

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

Frage 178

Frage
PSI-BLAST uses a position-specific scoring matrix
Antworten
  • True
  • False

Frage 179

Frage
UPGMA can be fitted with an evolutionary model
Antworten
  • True
  • False

Frage 180

Frage
microarrays assay gene expression by quantification of mRNA using hybridisation
Antworten
  • True
  • False

Frage 181

Frage
[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
Antworten
  • quantile

Frage 182

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

Frage 183

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

Frage 184

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

Frage 185

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

Frage 186

Frage
organisms have 1 genome and 1 proteome
Antworten
  • True
  • False

Frage 187

Frage
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]
Antworten
  • isoelectric
  • point

Frage 188

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

Frage 189

Frage
Sensitivity is good in 2DGE as the dye is linearly incorporated
Antworten
  • True
  • False

Frage 190

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

Frage 191

Frage
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
Antworten
  • ester
  • reporter
  • balancer

Frage 192

Frage
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.
Antworten
  • True
  • False

Frage 193

Frage
iTRAQ is a relative quantification method in LC-MS
Antworten
  • True
  • False

Frage 194

Frage
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.
Antworten
  • proprietary
  • boxes

Frage 195

Frage
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
Antworten
  • statistically
  • functionally

Frage 196

Frage
the function of a protein depends on its [blank_start]structure[blank_end]
Antworten
  • structure

Frage 197

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

Frage 198

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

Frage 199

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

Frage 200

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