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Bioinformatics

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Test sobre Bioinformatics, creado por lauren beck el 19/01/2020.
lauren beck
Test por lauren beck, actualizado hace más de 1 año
lauren beck
Creado por lauren beck hace casi 5 años
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Resumen del Recurso

Pregunta 1

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

Pregunta 2

Pregunta
[blank_start]Sanger sequencing[blank_end] is an example of a first generation sequencing technology
Respuesta
  • Sanger sequencing

Pregunta 3

Pregunta
Sanger sequencing has been automated by fluorescent labelling
Respuesta
  • True
  • False

Pregunta 4

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

Pregunta 5

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

Pregunta 6

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

Pregunta 7

Pregunta
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
Respuesta
  • True
  • False

Pregunta 8

Pregunta
454 pyrosequencing and ion torrent use solid-phase bridge PCR
Respuesta
  • True
  • False

Pregunta 9

Pregunta
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]
Respuesta
  • pH
  • light

Pregunta 10

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

Pregunta 11

Pregunta
[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
Respuesta
  • human
  • genome
  • project
  • encode
  • 1000
  • genomes
  • project

Pregunta 12

Pregunta
[blank_start]shotgun[blank_end] [blank_start]sequencing[blank_end] is the most common sequencing approach for whole genomes
Respuesta
  • shotgun
  • sequencing

Pregunta 13

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

Pregunta 14

Pregunta
the de bruijn graph method is a greedy method of assembly
Respuesta
  • True
  • False

Pregunta 15

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

Pregunta 16

Pregunta
sequence assembly can be...
Respuesta
  • ab initio
  • de novo
  • read mapping

Pregunta 17

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

Pregunta 18

Pregunta
Genomes always need to be finished
Respuesta
  • True
  • False

Pregunta 19

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

Pregunta 20

Pregunta
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
Respuesta
  • reads
  • coverage
  • genome length
  • read length
  • coverage
  • reads
  • genome length
  • read length

Pregunta 21

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

Pregunta 22

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

Pregunta 23

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

Pregunta 24

Pregunta
[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
Respuesta
  • Burrows
  • wheeler

Pregunta 25

Pregunta
We always need to assemble the genome in metagenomics experiments
Respuesta
  • True
  • False

Pregunta 26

Pregunta
raw sequencing data from sequencing experiments are saved in the sequence read archive
Respuesta
  • True
  • False

Pregunta 27

Pregunta
annotated sequence data from sequencing experiments are saved in GenBank and EMBL
Respuesta
  • True
  • False

Pregunta 28

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

Pregunta 29

Pregunta
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
Respuesta
  • True
  • False

Pregunta 30

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

Pregunta 31

Pregunta
gene prediction involves finding UTRs and alternative splice isoforms
Respuesta
  • True
  • False

Pregunta 32

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

Pregunta 33

Pregunta
ab initio gene finding approaches are more accurate for eukaryotes than prokaryotes
Respuesta
  • True
  • False

Pregunta 34

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

Pregunta 35

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

Pregunta 36

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

Pregunta 37

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

Pregunta 38

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

Pregunta 39

Pregunta
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]
Respuesta
  • 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

Pregunta 40

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

Pregunta 41

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

Pregunta 42

Pregunta
introns, intergenic regions and pseudogenes are highly conserved and intolerant to change
Respuesta
  • True
  • False

Pregunta 43

Pregunta
Gene duplicates experience relaxed evolutionary constraints
Respuesta
  • True
  • False

Pregunta 44

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

Pregunta 45

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

Pregunta 46

Pregunta
gene duplication can lead to [blank_start]nonfunctionalisation[blank_end] [blank_start]neofunctionalisation[blank_end] or [blank_start]subfunctionalisation[blank_end]
Respuesta
  • nonfunctionalisation
  • neofunctionalisation
  • subfunctionalisation

Pregunta 47

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

Pregunta 48

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

Pregunta 49

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

Pregunta 50

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

Pregunta 51

Pregunta
homology is a measure of similarity
Respuesta
  • True
  • False

Pregunta 52

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

Pregunta 53

Pregunta
what kind of mutations are more common?
Respuesta
  • 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

Pregunta 54

Pregunta
PAM and BLOSUM are example of [blank_start]substitution[blank_end] [blank_start]matrices[blank_end]
Respuesta
  • substitution
  • matrices

Pregunta 55

Pregunta
1 PAM is 1% similarity
Respuesta
  • True
  • False

Pregunta 56

Pregunta
PAM is better for [blank_start]global[blank_end] alignments whilst BLOSUM is better for [blank_start]local[blank_end] alignments
Respuesta
  • global
  • local

Pregunta 57

Pregunta
BLOSUM matrices are derived from the [blank_start]BLOCKS[blank_end] database
Respuesta
  • BLOCKS

Pregunta 58

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

Pregunta 59

Pregunta
A local alignment tries to align all the residues in a sequence
Respuesta
  • True
  • False

Pregunta 60

Pregunta
Dynamic programming is used for [blank_start]exact[blank_end] alignment methods
Respuesta
  • exact

Pregunta 61

Pregunta
Needleman-Wunsch is a [blank_start]global[blank_end] alignment algorithm
Respuesta
  • global

Pregunta 62

Pregunta
Smith-waterman is a local alignment algorithm
Respuesta
  • True
  • False

Pregunta 63

Pregunta
The trajectory refers to the traceback arrows in a trajectory table
Respuesta
  • True
  • False

Pregunta 64

Pregunta
BLAST and FASTA are examples of [blank_start]heuristic[blank_end] alignment methods
Respuesta
  • heuristic

Pregunta 65

Pregunta
Exact alignment methods are not guaranteed to find an optimal solution
Respuesta
  • True
  • False

Pregunta 66

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

Pregunta 67

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

Pregunta 68

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

Pregunta 69

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

Pregunta 70

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

Pregunta 71

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

Pregunta 72

Pregunta
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
Respuesta
  • profile
  • pattern
  • pattern
  • profile

Pregunta 73

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

Pregunta 74

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

Pregunta 75

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

Pregunta 76

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

Pregunta 77

Pregunta
[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
Respuesta
  • Bootstrap
  • values

Pregunta 78

Pregunta
[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
Respuesta
  • WPGMA

Pregunta 79

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

Pregunta 80

Pregunta
[blank_start]normalisation[blank_end] aims to remove technical variation existing in microarray experiments
Respuesta
  • normalisation

Pregunta 81

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

Pregunta 82

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

Pregunta 83

Pregunta
[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
Respuesta
  • Benjamin
  • Hochberg
  • FDR

Pregunta 84

Pregunta
Benjamin-Hochberg FDR modifies [blank_start]P[blank_end]-values
Respuesta
  • P

Pregunta 85

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

Pregunta 86

Pregunta
[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
Respuesta
  • Poly
  • A
  • selection

Pregunta 87

Pregunta
RNA-sequencing relies on reverse transcription
Respuesta
  • True
  • False

Pregunta 88

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

Pregunta 89

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

Pregunta 90

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

Pregunta 91

Pregunta
microarrays can be used to discover novel transcripts
Respuesta
  • True
  • False

Pregunta 92

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

Pregunta 93

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

Pregunta 94

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

Pregunta 95

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

Pregunta 96

Pregunta
[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
Respuesta
  • DIGE

Pregunta 97

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

Pregunta 98

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

Pregunta 99

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

Pregunta 100

Pregunta
[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
Respuesta
  • peptide
  • mass
  • fingerprinting

Pregunta 101

Pregunta
2DGE can be used to identify membrane proteins
Respuesta
  • True
  • False

Pregunta 102

Pregunta
2DGE cannot be used to show post-translational modifications
Respuesta
  • True
  • False

Pregunta 103

Pregunta
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
Respuesta
  • trypsin

Pregunta 104

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

Pregunta 105

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

Pregunta 106

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

Pregunta 107

Pregunta
the intensity of peaks in MS can be used to quantify proteins
Respuesta
  • True
  • False

Pregunta 108

Pregunta
[blank_start]hydrophobicity[blank_end] is the main driving force of protein folding process
Respuesta
  • hydrophobicity

Pregunta 109

Pregunta
secondary structure refers to global interactions within a protein
Respuesta
  • True
  • False

Pregunta 110

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

Pregunta 111

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

Pregunta 112

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

Pregunta 113

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

Pregunta 114

Pregunta
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
Respuesta
  • Ramachandran
  • plot

Pregunta 115

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

Pregunta 116

Pregunta
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]
Respuesta
  • 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

Pregunta 117

Pregunta
mainly alpha and mainly beta are examples of CATH folds
Respuesta
  • True
  • False

Pregunta 118

Pregunta
3D protein structure prediction is treated as a machine learning problem
Respuesta
  • True
  • False

Pregunta 119

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

Pregunta 120

Pregunta
Dynamic programming is an optimisation method
Respuesta
  • True
  • False

Pregunta 121

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

Pregunta 122

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

Pregunta 123

Pregunta
[blank_start]PSIPRED[blank_end] is the most popular secondary structure prediction software
Respuesta
  • PSIPRED

Pregunta 124

Pregunta
PSIPRED uses hidden markov models
Respuesta
  • True
  • False

Pregunta 125

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

Pregunta 126

Pregunta
[blank_start]solvent[blank_end] [blank_start]accessibility[blank_end] is the amount of surface exposed of each residue
Respuesta
  • solvent
  • accessibility

Pregunta 127

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

Pregunta 128

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

Pregunta 129

Pregunta
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
Respuesta
  • True
  • False

Pregunta 130

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

Pregunta 131

Pregunta
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
Respuesta
  • homology
  • modelling
  • ab
  • initio

Pregunta 132

Pregunta
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,
Respuesta
  • decoys

Pregunta 133

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

Pregunta 134

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

Pregunta 135

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

Pregunta 136

Pregunta
in a network, sink nodes have high in degree and sources have a high out degree
Respuesta
  • True
  • False

Pregunta 137

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

Pregunta 138

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

Pregunta 139

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

Pregunta 140

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

Pregunta 141

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

Pregunta 142

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

Pregunta 143

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

Pregunta 144

Pregunta
a random Boolean network is undirected
Respuesta
  • True
  • False

Pregunta 145

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

Pregunta 146

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

Pregunta 147

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

Pregunta 148

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

Pregunta 149

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

Pregunta 150

Pregunta
PathExpand and TopoGSA are examples of network [blank_start]refinement[blank_end] packages
Respuesta
  • refinement

Pregunta 151

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

Pregunta 152

Pregunta
An Arc network is more scalable than a Hive network
Respuesta
  • True
  • False

Pregunta 153

Pregunta
community detection is also known as [blank_start]clustering[blank_end]
Respuesta
  • clustering

Pregunta 154

Pregunta
[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
Respuesta
  • clustering

Pregunta 155

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

Pregunta 156

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

Pregunta 157

Pregunta
there are [blank_start]20[blank_end] amino acids used in biological systems
Respuesta
  • 20

Pregunta 158

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

Pregunta 159

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

Pregunta 160

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

Pregunta 161

Pregunta
Third generation sequencing involves a PCR step
Respuesta
  • True
  • False

Pregunta 162

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

Pregunta 163

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

Pregunta 164

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

Pregunta 165

Pregunta
the coverage equation often underestimates the number of reads necessary
Respuesta
  • True
  • False

Pregunta 166

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

Pregunta 167

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

Pregunta 168

Pregunta
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
Respuesta
  • :
  • .

Pregunta 169

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

Pregunta 170

Pregunta
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]
Respuesta
  • E
  • value

Pregunta 171

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

Pregunta 172

Pregunta
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
Respuesta
  • iterative

Pregunta 173

Pregunta
In a progression MSA, the original mapping can be changed
Respuesta
  • True
  • False

Pregunta 174

Pregunta
progressive multiple sequence alignment strategies use pairwise alignments
Respuesta
  • True
  • False

Pregunta 175

Pregunta
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
Respuesta
  • kimura
  • distance

Pregunta 176

Pregunta
muscle uses WPGMA to make alignments
Respuesta
  • True
  • False

Pregunta 177

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

Pregunta 178

Pregunta
PSI-BLAST uses a position-specific scoring matrix
Respuesta
  • True
  • False

Pregunta 179

Pregunta
UPGMA can be fitted with an evolutionary model
Respuesta
  • True
  • False

Pregunta 180

Pregunta
microarrays assay gene expression by quantification of mRNA using hybridisation
Respuesta
  • True
  • False

Pregunta 181

Pregunta
[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
Respuesta
  • quantile

Pregunta 182

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

Pregunta 183

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

Pregunta 184

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

Pregunta 185

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

Pregunta 186

Pregunta
organisms have 1 genome and 1 proteome
Respuesta
  • True
  • False

Pregunta 187

Pregunta
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]
Respuesta
  • isoelectric
  • point

Pregunta 188

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

Pregunta 189

Pregunta
Sensitivity is good in 2DGE as the dye is linearly incorporated
Respuesta
  • True
  • False

Pregunta 190

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

Pregunta 191

Pregunta
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
Respuesta
  • ester
  • reporter
  • balancer

Pregunta 192

Pregunta
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.
Respuesta
  • True
  • False

Pregunta 193

Pregunta
iTRAQ is a relative quantification method in LC-MS
Respuesta
  • True
  • False

Pregunta 194

Pregunta
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.
Respuesta
  • proprietary
  • boxes

Pregunta 195

Pregunta
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
Respuesta
  • statistically
  • functionally

Pregunta 196

Pregunta
the function of a protein depends on its [blank_start]structure[blank_end]
Respuesta
  • structure

Pregunta 197

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

Pregunta 198

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

Pregunta 199

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

Pregunta 200

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