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Quiz on Bioinformatics, created by lauren beck on 19/01/2020.

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Bioinformatics

Bioinformatics

Question 1 of 200

1

Which of the following are sequence elements that algorithms can exploit to search for genes in a prokaryotic genome?

Select one or more of the following:

  • TFIIB recognition element

  • TATA box at -10

  • ATG start codon

  • STOP codon

  • downstream core promoter element at +30

  • initiator element around transcription start site

Explanation

Question 2 of 200

1

Fill the blank space to complete the text.

is an example of a first generation sequencing technology

Explanation

Question 3 of 200

1

Sanger sequencing has been automated by fluorescent labelling

Select one of the following:

  • True
  • False

Explanation

Question 4 of 200

1

Which of the following are advantages of sanger sequencing?

Select one or more of the following:

  • high accuracy

  • good for short sequences

  • high throughput

  • cheap

  • long read length

Explanation

Question 5 of 200

1

select the technologies that are second generation sequencing methods

Select one or more of the following:

  • Sanger

  • 454 pyrosequencing

  • Ilumina

  • Ion torrent

  • nanopore

  • PacBio

Explanation

Question 6 of 200

1

Which of the following are limitations of 454 pyrosequencing?

Select one or more of the following:

  • slow sample preparation

  • lower throughput than sanger

  • shorter read lengths than sanger

  • homopolymer errors

Explanation

Question 7 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 8 of 200

1

454 pyrosequencing and ion torrent use solid-phase bridge PCR

Select one of the following:

  • True
  • False

Explanation

Question 9 of 200

1

Fill the blank spaces to complete the text.

Ion torrent detects the incorporation of a base based on whereas 454 pyrosequencing detects the incorporation of a base based on

Explanation

Question 10 of 200

1

What are the advantages of third generation sequencing technologies?

Select one or more of the following:

  • High accuracy

  • high throughput

  • longer read length

  • Low cost

  • minimal sample preparation

Explanation

Question 11 of 200

1

Fill the blank spaces to complete the text.

and are all examples of large scale genome sequencing projects

Explanation

Question 12 of 200

1

Fill the blank spaces to complete the text.

is the most common sequencing approach for whole genomes

Explanation

Question 13 of 200

1

Select from the dropdown list to complete the text.

a ( contig, scaffold, read, coverage ) is a set of overlapping DNA fragments that together represent a consensus region of DNA

Explanation

Question 14 of 200

1

the de bruijn graph method is a greedy method of assembly

Select one of the following:

  • True
  • False

Explanation

Question 15 of 200

1

Fill the blank space to complete the text.

is the parameter used in the de bruijn graph assembly algorithm

Explanation

Question 16 of 200

1

sequence assembly can be...

Select one or more of the following:

  • ab initio

  • de novo

  • read mapping

Explanation

Question 17 of 200

1

Which of the following are de bruijn graph sequence assemblers?

Select one or more of the following:

  • Celera

  • GigAssembler

  • Velvet

  • SPAdes

Explanation

Question 18 of 200

1

Genomes always need to be finished

Select one of the following:

  • True
  • False

Explanation

Question 19 of 200

1

hybrid sequencing is an effective way of closing gaps in genome assembly as different technologies are biased in sequencing in different ways

Select one of the following:

  • True
  • False

Explanation

Question 20 of 200

1

Select from the dropdown lists to complete the text.

in the equation N = (a x g) / L
N is the ( reads, coverage, genome length, read length ) a is the ( coverage, reads, genome length, read length ) g is the genome length and L is the read length

Explanation

Question 21 of 200

1

Which of the following are examples of challenges faced during sequence assembly?

Select one or more of the following:

  • sequencing errors

  • shotgun fragmenting is not random

  • repeated regions

  • computational power

  • throughput

  • cost

Explanation

Question 22 of 200

1

Why can't BLAST be used for short read mapping to assemble our reads using a reference genome?

Select one of the following:

  • it costs too much and is highly inaccurate

  • it is not compatible

  • it takes too long and is not good at finding close matches

Explanation

Question 23 of 200

1

when might short-read mapping be beneficial to use?

Select one or more of the following:

  • for RNA-sequencing experiments

  • for chipping experiments

  • to assemble a whole genome

  • to find open reading frames

Explanation

Question 24 of 200

1

Fill the blank spaces to complete the text.

- 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

Explanation

Question 25 of 200

1

We always need to assemble the genome in metagenomics experiments

Select one of the following:

  • True
  • False

Explanation

Question 26 of 200

1

raw sequencing data from sequencing experiments are saved in the sequence read archive

Select one of the following:

  • True
  • False

Explanation

Question 27 of 200

1

annotated sequence data from sequencing experiments are saved in GenBank and EMBL

Select one of the following:

  • True
  • False

Explanation

Question 28 of 200

1

Which of the following are legitimate methods of assessing a sequence assembly?

Select one or more of the following:

  • the N50 statistic

  • principle component analysis

  • average gap size

  • average number of gaps per scaffold

  • coverage

  • hierarchical clusterin

Explanation

Question 29 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 30 of 200

1

sequence annotation involves identifying...

Select one or more of the following:

  • read lengths

  • coverage

  • CDSs

  • promoters

  • ribosome binding sites

  • introns

  • exons

Explanation

Question 31 of 200

1

gene prediction involves finding UTRs and alternative splice isoforms

Select one of the following:

  • True
  • False

Explanation

Question 32 of 200

1

what are the 2 major approaches for gene finding?

Select one or more of the following:

  • ab initio

  • comparative proteomics

  • comparative genomics

  • de novo

Explanation

Question 33 of 200

1

ab initio gene finding approaches are more accurate for eukaryotes than prokaryotes

Select one of the following:

  • True
  • False

Explanation

Question 34 of 200

1

Fill the blank spaces to complete the text.

the gene finding tools Glimmer and GeneScan use models

Explanation

Question 35 of 200

1

which of the following make eukaryotic gene finding more difficult than prokaryotic gene finding?

Select one or more of the following:

  • high number of repeats

  • introns

  • exons

  • highly compact

  • alternative splicing

Explanation

Question 36 of 200

1

What measures can be used to assess gene prediction?

Select one or more of the following:

  • sensitivity

  • specificity

  • accuracy

  • N50 statistic

Explanation

Question 37 of 200

1

There is a trade-off when it comes to the specificity and sensitivity of gene prediction tools

Select one of the following:

  • True
  • False

Explanation

Question 38 of 200

1

Select from the dropdown list to complete the text.

( prokka, genescan, glimmer, genie ) is a genome annotation pipeline good for prokaryotes and small eukaryotes

Explanation

Question 39 of 200

1

Select from the dropdown lists to complete the text.

order the types of mutation in terms of relative frequency:
1. ( point, deletion, inversion, insertion, translocation, duplication )
2. ( deletion, point, insertion, inversion, duplication, translocation )
3. ( duplication, point, deletion, inversion, insertion, translocation )
4. ( inversion, insertion, point, deletion, translocation, duplication )
5. ( insertion, inversion, translocation, duplication, point, deletion )
6. ( translocation, inversion, insertion, duplication, point, deletion )

Explanation

Question 40 of 200

1

Fill the blank space to complete the text.

silent, missense and nonsense are all types of mutation

Explanation

Question 41 of 200

1

nonsense mutations can be conservative or non-conservative (similar AA or not)

Select one of the following:

  • True
  • False

Explanation

Question 42 of 200

1

introns, intergenic regions and pseudogenes are highly conserved and intolerant to change

Select one of the following:

  • True
  • False

Explanation

Question 43 of 200

1

Gene duplicates experience relaxed evolutionary constraints

Select one of the following:

  • True
  • False

Explanation

Question 44 of 200

1

when does gene duplication occur in bacteria?

Select one of the following:

  • in response to favourable conditions

  • in response to stress

  • in response to an internal stimulus

  • linearly over evolutionary time

Explanation

Question 45 of 200

1

Select from the dropdown list to complete the text.

( duplication, point mutation, inversion, insertion, deletion ) is an essential mutation for evolutionary change to occur in eukaryotes

Explanation

Question 46 of 200

1

Fill the blank spaces to complete the text.

gene duplication can lead to or

Explanation

Question 47 of 200

1

which of the following are sources of variation in prokaryotes?

Select one or more of the following:

  • lateral gene transfer

  • endosymbiosis

  • mutations

Explanation

Question 48 of 200

1

genes that share a common ancestor are said to be what?

Select one or more of the following:

  • homologs

  • paralogs

  • orthologs

  • xenologs

Explanation

Question 49 of 200

1

genes that have diverged as a result of speciation are said to be what?

Select one or more of the following:

  • homologs

  • orthologs

  • paralogs

  • xenologs

Explanation

Question 50 of 200

1

genes within the same genome created as a result of gene duplication are said to be what?

Select one or more of the following:

  • homologs

  • orthologs

  • paralogs

  • xenologs

Explanation

Question 51 of 200

1

homology is a measure of similarity

Select one of the following:

  • True
  • False

Explanation

Question 52 of 200

1

which of the following are simplistic measure of similarity when it comes to measuring sequence similarity?

Select one or more of the following:

  • hamming distance

  • sequence identity

  • levenshtein distance

  • PAM250

  • BLOSUM62

Explanation

Question 53 of 200

1

what kind of mutations are more common?

Select one or more of the following:

  • 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

Explanation

Question 54 of 200

1

Fill the blank spaces to complete the text.

PAM and BLOSUM are example of

Explanation

Question 55 of 200

1

1 PAM is 1% similarity

Select one of the following:

  • True
  • False

Explanation

Question 56 of 200

1

Fill the blank spaces to complete the text.

PAM is better for alignments whilst BLOSUM is better for alignments

Explanation

Question 57 of 200

1

Fill the blank space to complete the text.

BLOSUM matrices are derived from the database

Explanation

Question 58 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 59 of 200

1

A local alignment tries to align all the residues in a sequence

Select one of the following:

  • True
  • False

Explanation

Question 60 of 200

1

Fill the blank space to complete the text.

Dynamic programming is used for alignment methods

Explanation

Question 61 of 200

1

Fill the blank space to complete the text.

Needleman-Wunsch is a alignment algorithm

Explanation

Question 62 of 200

1

Smith-waterman is a local alignment algorithm

Select one of the following:

  • True
  • False

Explanation

Question 63 of 200

1

The trajectory refers to the traceback arrows in a trajectory table

Select one of the following:

  • True
  • False

Explanation

Question 64 of 200

1

Fill the blank space to complete the text.

BLAST and FASTA are examples of alignment methods

Explanation

Question 65 of 200

1

Exact alignment methods are not guaranteed to find an optimal solution

Select one of the following:

  • True
  • False

Explanation

Question 66 of 200

1

K-tuple alignment methods are a family of approximate alignment methods, and BLAST is part of the family

Select one of the following:

  • True
  • False

Explanation

Question 67 of 200

1

Fill the blank space to complete the text.

a approach is taken with multiple sequence alignment because an exact approach has complexity O(L^N)

Explanation

Question 68 of 200

1

Fill the blank space to complete the text.

progressive, iterative and statistical are all approaches used for

Explanation

Question 69 of 200

1

Which of the following are examples of progressive alignment algorithms?

Select one or more of the following:

  • T-coffee

  • Clustal omega

  • Clustal W

  • Muscle

Explanation

Question 70 of 200

1

Which of the following algorithms takes a hybrid approach for multiple sequence alignment?

Select one of the following:

  • T-coffee

  • Muscle

  • Clustal omega

  • Clustal W

Explanation

Question 71 of 200

1

Fill the blank space to complete the text.

A is part of a protein sequence associated with a particular biological function

Explanation

Question 72 of 200

1

Select from the dropdown lists to complete the text.

A ( pattern, profile ) is a qualitative description of a motif
A ( profile, pattern ) is a quantitative description of a motif

Explanation

Question 73 of 200

1

Which of the following databases describe motifs in terms of pattern and profile?

Select one or more of the following:

  • Pfam

  • PROSITE

  • InterPro

  • GeneBank

  • EMBL

  • BLOCKS

Explanation

Question 74 of 200

1

PSI-BLAST is more powerful than BLAST for picking up distant relationships between sequences

Select one of the following:

  • True
  • False

Explanation

Question 75 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 76 of 200

1

Which of the following are examples of distance-based tree building methods?

Select one or more of the following:

  • Maximum likelihood

  • Maximum parsimony

  • UPGMA

  • WPGMA

  • Bayesian inference

Explanation

Question 77 of 200

1

Fill the blank spaces to complete the text.

can be added to branches in phylogenetic trees to summarise the degree of certainty for a given branching

Explanation

Question 78 of 200

1

Fill the blank space to complete the text.

uses a flat average whilst UPGMA uses a weighted average that takes into account the number of taxa in a group

Explanation

Question 79 of 200

1

microarrays and RNA-sequencing are examples of what kind of experiments?

Select one of the following:

  • genomics

  • transcriptomics

  • proteomics

  • phylogenetics

Explanation

Question 80 of 200

1

Fill the blank space to complete the text.

aims to remove technical variation existing in microarray experiments

Explanation

Question 81 of 200

1

Which of the following are methods for quality control to remove outliers from microarray experiments?

Select one or more of the following:

  • N50 statistic

  • hierarchical clustering

  • normalisation

  • principle component analysis

  • probeset QC

  • multiple testing correction

Explanation

Question 82 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 83 of 200

1

Fill the blank spaces to complete the text.

- is the most common multiple testing correction used in microarray, RNA-seq and proteomics experiments

Explanation

Question 84 of 200

1

Fill the blank space to complete the text.

Benjamin-Hochberg FDR modifies -values

Explanation

Question 85 of 200

1

Which of the following are not advantages for RNA-seq experiments over microarrays?

Select one or more of the following:

  • can search for unknown genes

  • can detect very scarce transcripts

  • lower technical variation

  • lower background noise

  • can sequence whole proteome

Explanation

Question 86 of 200

1

Fill the blank spaces to complete the text.

- gets rid of uninteresting, abundant RNA such as rRNA and haemoglobin RNA in blood samples in preparation for RNA-seq experiment

Explanation

Question 87 of 200

1

RNA-sequencing relies on reverse transcription

Select one of the following:

  • True
  • False

Explanation

Question 88 of 200

1

RNA-sequencing experiments are quantifiable - the sequencing reads in the library are proportional to the abundance of RNA

Select one of the following:

  • True
  • False

Explanation

Question 89 of 200

1

Fill the blank space to complete the text.

RPKM and FPKM are examples of tools used following an RNA-sequencing experiment

Explanation

Question 90 of 200

1

T-tests can be used to analyse microarray and RNA-seq data as both are continuous

Select one of the following:

  • True
  • False

Explanation

Question 91 of 200

1

microarrays can be used to discover novel transcripts

Select one of the following:

  • True
  • False

Explanation

Question 92 of 200

1

transcriptomics is used instead of proteomics as the transcript level always correlates to the protein abundance

Select one of the following:

  • True
  • False

Explanation

Question 93 of 200

1

Fill the blank spaces to complete the text.

the two main approaches in expression proteomics experiments are up and down experiments

Explanation

Question 94 of 200

1

Which of the following are experimental strategies used in proteomics?

Select one or more of the following:

  • liquid chromatography tandem MS

  • 2DGE

  • Microarrays

  • RNA-sequencing

Explanation

Question 95 of 200

1

Which of the following are disadvantages of 2DGE?

Select one or more of the following:

  • expensive

  • time-consuming

  • limited sensitivity

  • limited resolution

  • low reproducibility

Explanation

Question 96 of 200

1

Fill the blank space to complete the text.

is a variation of 2DGE whereby multiple samples are ran on one gel but are differentially labelled to eliminate running difference between gels

Explanation

Question 97 of 200

1

Technical variation is higher in microarrays and RNA-seq than 2DGE and liquid chromatography tandem MS

Select one of the following:

  • True
  • False

Explanation

Question 98 of 200

1

Fill the blank spaces to complete the text.

in 2DGE, proteins are separated based first on then on

Explanation

Question 99 of 200

1

Select from the dropdown list to complete the text.

progenesis is a software used in ( 2DGE, microarray, RNA-seq, HPLC ) experiments

Explanation

Question 100 of 200

1

Fill the blank spaces to complete the text.

- is used to identify which proteins are contained within spots on a gel from a 2DGE experiment

Explanation

Question 101 of 200

1

2DGE can be used to identify membrane proteins

Select one of the following:

  • True
  • False

Explanation

Question 102 of 200

1

2DGE cannot be used to show post-translational modifications

Select one of the following:

  • True
  • False

Explanation

Question 103 of 200

1

Fill the blank space to complete the text.

in a proteomics experiment, proteins are first isolated then digested using an enzyme such as as it cuts in a predictable ways

Explanation

Question 104 of 200

1

in a peptide-mass fingerprinting experiment, resulting peak-lists can be the same for very similar proteins

Select one of the following:

  • True
  • False

Explanation

Question 105 of 200

1

in tandem MS, when fragments are introduced they are broken up by argon gas, which preferentially breaks peptide bonds

Select one of the following:

  • True
  • False

Explanation

Question 106 of 200

1

Which of the following databases of hypothetical spectra is used to identify peptides from an MS experiment?

Select one of the following:

  • Genescan

  • InterPro

  • MASCOT

  • BLOCKS

  • PRINTS

  • iTRAQ

Explanation

Question 107 of 200

1

the intensity of peaks in MS can be used to quantify proteins

Select one of the following:

  • True
  • False

Explanation

Question 108 of 200

1

Fill the blank space to complete the text.

is the main driving force of protein folding process

Explanation

Question 109 of 200

1

secondary structure refers to global interactions within a protein

Select one of the following:

  • True
  • False

Explanation

Question 110 of 200

1

Fill the blank spaces to complete the text.

helix, sheet and are the 3 secondary structure states

Explanation

Question 111 of 200

1

Fill the blank space to complete the text.

protein are subunits within a protein with quasi-independent folding stability

Explanation

Question 112 of 200

1

Fill the blank space to complete the text.

the structure refers to proteins formed from several subunits or monomers

Explanation

Question 113 of 200

1

Fill the blank space to complete the text.

protein structures solved by NMR or crystallography are saved as files

Explanation

Question 114 of 200

1

Fill the blank spaces to complete the text.

a visualises and clusters residues of an amino acid sequence based on psi and phi angles of the residue backbone

Explanation

Question 115 of 200

1

CATH, SCOP and FSSP/DDD are all examples of what?

Select one of the following:

  • tertiary structure classification methods

  • protein structure prediction assessment

  • databases containing sequence information

  • protein data banks

Explanation

Question 116 of 200

1

Select from the dropdown lists to complete the text.

the levels of hierarchy in the CATH system to catalogue proteins are ordered from bottom to top as follows:
1. ( class, domain, architecture, superfamily, fold )
2. ( architecture, class, domain, fold, superfamily )
3. ( fold, domain, class, architecture, superfamily )
4. ( superfamily, architecture, domain, class, fold )
5. ( domain, class, architecture, fold, superfamily )

Explanation

Question 117 of 200

1

mainly alpha and mainly beta are examples of CATH folds

Select one of the following:

  • True
  • False

Explanation

Question 118 of 200

1

3D protein structure prediction is treated as a machine learning problem

Select one of the following:

  • True
  • False

Explanation

Question 119 of 200

1

machine learning in the context of protein structure prediction aims to minimise the energy function

Select one of the following:

  • True
  • False

Explanation

Question 120 of 200

1

Dynamic programming is an optimisation method

Select one of the following:

  • True
  • False

Explanation

Question 121 of 200

1

Which of the following are types of machine learning?

Select one or more of the following:

  • Hidden markov models

  • artificial neural networks

  • rule learning

  • position specific scoring

  • multiple testing correction

Explanation

Question 122 of 200

1

Fill the blank space to complete the text.

a is similar to a substitution matrix but specifically tailored to the sequence being aligned

Explanation

Question 123 of 200

1

Fill the blank space to complete the text.

is the most popular secondary structure prediction software

Explanation

Question 124 of 200

1

PSIPRED uses hidden markov models

Select one of the following:

  • True
  • False

Explanation

Question 125 of 200

1

Fill the blank spaces to complete the text.

is the number of connections a residue in a protein has

Explanation

Question 126 of 200

1

Fill the blank spaces to complete the text.

is the amount of surface exposed of each residue

Explanation

Question 127 of 200

1

which of the following are the broad approaches for 3D PSP?

Select one or more of the following:

  • De novo

  • Ab initio

  • template-based

  • machine learning

Explanation

Question 128 of 200

1

which 3 ways can a template by identified for 3D PSP?

Select one or more of the following:

  • homology modelling

  • profile-base methods

  • machine learning

  • threading

  • ab initio modelling

Explanation

Question 129 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 130 of 200

1

in 3D PSP, profile-based methods make profiles for residues in a sequence based on...

Select one or more of the following:

  • secondary structure

  • hydrophobicity

  • acidity

  • solvent accessibility

  • tertiary structure

Explanation

Question 131 of 200

1

Fill the blank spaces to complete the text.

in 3D PSP, fragment assembly combines with methods

Explanation

Question 132 of 200

1

Fill the blank space to complete the text.

in fragment assembly, 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,

Explanation

Question 133 of 200

1

Fill the blank space to complete the text.

I-Tasser is a used for protein structure prediction

Explanation

Question 134 of 200

1

Fill the blank spaces to complete the text.

a network is a graph consisting of a series of connect by

Explanation

Question 135 of 200

1

Fill the blank space to complete the text.

in a biological network, genes, proteins and cell types can be depicted as

Explanation

Question 136 of 200

1

in a network, sink nodes have high in degree and sources have a high out degree

Select one of the following:

  • True
  • False

Explanation

Question 137 of 200

1

Which of the following is not a type of degree distribution in a network?

Select one of the following:

  • constant

  • scale-free

  • random

  • betweenness

Explanation

Question 138 of 200

1

In a network, the distance can be defined by Pajek or Watts

Select one of the following:

  • True
  • False

Explanation

Question 139 of 200

1

The longest shortest path between all pairs of nodes is...

Select one of the following:

  • Pajeks diameter

  • Pajeks distance

  • Watts diameter

  • Watts distance

Explanation

Question 140 of 200

1

Fill the blank space to complete the text.

the is defined by the number of edges as a fraction of the number of possible edges

Explanation

Question 141 of 200

1

Which of the following are measures of centrality of a network?

Select one or more of the following:

  • degree

  • betweenness

  • closeness

  • distance

  • diameter

Explanation

Question 142 of 200

1

The betweenness centrality is a fraction of the shortest paths of the network for which a certain node is a member of

Select one of the following:

  • True
  • False

Explanation

Question 143 of 200

1

Fill the blank spaces to complete the text.

rewards nodes from which within a few edges, any node can be accessed

Explanation

Question 144 of 200

1

a random Boolean network is undirected

Select one of the following:

  • True
  • False

Explanation

Question 145 of 200

1

A random Boolean network can be used to study dynamic processes such as gene expression

Select one of the following:

  • True
  • False

Explanation

Question 146 of 200

1

Fill the blank space to complete the text.

an network uses data from high-quality databases such as BioGrid as well as our own experimental data

Explanation

Question 147 of 200

1

Fill the blank spaces to complete the text.

Gene co-expression networks are built using by

Explanation

Question 148 of 200

1

In gene co-expression networks, similarity in expression across samples is usually computed by

Select one of the following:

  • pearson's correlation

  • principle component analysis

  • guilt-by-association

  • force

Explanation

Question 149 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 150 of 200

1

Fill the blank space to complete the text.

PathExpand and TopoGSA are examples of network packages

Explanation

Question 151 of 200

1

Fill the blank space to complete the text.

force, arc, circular and hive are all examples of network

Explanation

Question 152 of 200

1

An Arc network is more scalable than a Hive network

Select one of the following:

  • True
  • False

Explanation

Question 153 of 200

1

Fill the blank space to complete the text.

community detection is also known as

Explanation

Question 154 of 200

1

Fill the blank space to complete the text.

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

Explanation

Question 155 of 200

1

Fill the blank space to complete the text.

represent relationships in a computationally amenable way by providing controlled vocabulary of terms

Explanation

Question 156 of 200

1

Which of the following are ontologies used by GO to describe the associations of gene products

Select one or more of the following:

  • biological processes

  • cellular components

  • 3D structure

  • interaction partners

  • molecular functions

Explanation

Question 157 of 200

1

Fill the blank space to complete the text.

there are amino acids used in biological systems

Explanation

Question 158 of 200

1

Which of the following is not commonly used to assess sequencing methods?

Select one of the following:

  • read length

  • throughput

  • cost per base

  • cost of the machine

  • sample size

Explanation

Question 159 of 200

1

Which of the following is not a database combined in the INSDC major collection point for sequencing data?

Select one of the following:

  • EMBL-EBI

  • NCBI

  • NIG

  • GenBank

Explanation

Question 160 of 200

1

Fill the blank space to complete the text.

Sanger, 454, ion torrent and ilumina sequencing all sequence by

Explanation

Question 161 of 200

1

Third generation sequencing involves a PCR step

Select one of the following:

  • True
  • False

Explanation

Question 162 of 200

1

Fill the blank space to complete the text.

the current gold-standard for shotgun sequencing assembly is a -fold coverage

Explanation

Question 163 of 200

1

Which of the following is not a reason for making sequence assembly difficult?

Select one of the following:

  • biased sequence composition

  • homopolymers

  • repeats

  • long reads

Explanation

Question 164 of 200

1

coverage assumes that DNA is randomly fragmented and all DNA is able to be sequenced.

Select one of the following:

  • True
  • False

Explanation

Question 165 of 200

1

the coverage equation often underestimates the number of reads necessary

Select one of the following:

  • True
  • False

Explanation

Question 166 of 200

1

Fill the blank spaces to complete the text.

silent mutations usually occur in the base of a

Explanation

Question 167 of 200

1

Fill the blank space to complete the text.

genes are those which are homologous and have been gained via horizontal gene transfer

Explanation

Question 168 of 200

1

Fill the blank spaces to complete the text.

in sequence alignments a represents a perfect match, a represents a similar AA and a blank space represents a larger AA change

Explanation

Question 169 of 200

1

Heuristic alignment methods are better when computational power is not a problem or for a small number of sequences

Select one of the following:

  • True
  • False

Explanation

Question 170 of 200

1

Fill the blank spaces to complete the text.

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 -

Explanation

Question 171 of 200

1

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in a MSA, the alignment table can be summarised in a single line, a pseudo sequence called the

Explanation

Question 172 of 200

1

Fill the blank space to complete the text.

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 method

Explanation

Question 173 of 200

1

In a progression MSA, the original mapping can be changed

Select one of the following:

  • True
  • False

Explanation

Question 174 of 200

1

progressive multiple sequence alignment strategies use pairwise alignments

Select one of the following:

  • True
  • False

Explanation

Question 175 of 200

1

Fill the blank spaces to complete the text.

the muscle MSA alignment method uses the matrix to make a global alignment during the improved progressive alignment

Explanation

Question 176 of 200

1

muscle uses WPGMA to make alignments

Select one of the following:

  • True
  • False

Explanation

Question 177 of 200

1

Fill the blank space to complete the text.

a can be incorporated into MSA and PSP algorithms to give better results

Explanation

Question 178 of 200

1

PSI-BLAST uses a position-specific scoring matrix

Select one of the following:

  • True
  • False

Explanation

Question 179 of 200

1

UPGMA can be fitted with an evolutionary model

Select one of the following:

  • True
  • False

Explanation

Question 180 of 200

1

microarrays assay gene expression by quantification of mRNA using hybridisation

Select one of the following:

  • True
  • False

Explanation

Question 181 of 200

1

Fill the blank space to complete the text.

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

Explanation

Question 182 of 200

1

Fill the blank space to complete the text.

principle component analysis reduces multi-dimensional data down to dimensions

Explanation

Question 183 of 200

1

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

Select one of the following:

  • True
  • False

Explanation

Question 184 of 200

1

which of the following does not encompass the same methods between microarrays and RNA-seq?

Select one or more of the following:

  • normalisation

  • quality control

  • statistical analysis

Explanation

Question 185 of 200

1

Fill the blank spaces to complete the text.

when analysing data from an RNA-seq experiment, DE-seq assumes a distribution

Explanation

Question 186 of 200

1

organisms have 1 genome and 1 proteome

Select one of the following:

  • True
  • False

Explanation

Question 187 of 200

1

Fill the blank spaces to complete the text.

in 2DGE, there is a pH gradient running left to right. Where a protein is positioned depends on its

Explanation

Question 188 of 200

1

in 2DGE, it is valid to compare spots between gels if the spot is absent on one of the gels

Select one of the following:

  • True
  • False

Explanation

Question 189 of 200

1

Sensitivity is good in 2DGE as the dye is linearly incorporated

Select one of the following:

  • True
  • False

Explanation

Question 190 of 200

1

LC-MS can be multidimensional, separating proteins based on more than 2 physiochemical properties

Select one of the following:

  • True
  • False

Explanation

Question 191 of 200

1

Fill the blank spaces to complete the text.

iTRAQ is used to label samples in order to quantify them. Tags are made up of an group to tag to the protein, a of varying sizes and a to balance the mass

Explanation

Question 192 of 200

1

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.

Select one of the following:

  • True
  • False

Explanation

Question 193 of 200

1

iTRAQ is a relative quantification method in LC-MS

Select one of the following:

  • True
  • False

Explanation

Question 194 of 200

1

Fill the blank spaces to complete the text.

data from LC-MS experiments have been locked in up until recently, meaning that specialist software was required to view and analyse data depending on the technology used.

Explanation

Question 195 of 200

1

Fill the blank spaces to complete the text.

spot profiles for LC-MS data can be clustered based on how similar their expression profiles are or based on how similar their function are

Explanation

Question 196 of 200

1

Fill the blank space to complete the text.

the function of a protein depends on its

Explanation

Question 197 of 200

1

Select from the dropdown list to complete the text.

a beta hairpin is an example of a ( supersecondary, secondary, tertiary, CATH, primary, domain ) structure

Explanation

Question 198 of 200

1

which of the following is not an example of a structural property of an individual residue that can be predicted

Select one or more of the following:

  • supersecondary structure

  • secondary structure

  • solvent accessibility

  • contact number

  • whether it is exposed on the surface

Explanation

Question 199 of 200

1

predicting structural aspects of protein residues is generally treated as an optimisation problem

Select one of the following:

  • True
  • False

Explanation

Question 200 of 200

1

Fill the blank space to complete the text.

is a technique used to link together non-contiguous series of genomic DNA

Explanation

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