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Flashcards in Final Exam Deck (49):
1

What is the difference between FASTQ files and FASTA files?

FASTQ files have a sequence of quality scores for each nucleotide base called in addition to the sequence identifier and run information and the sequence itself.

2

In NGS sequencing processing, as in the above example (FASTQ) readout, the Q scores it...?
A. Similar across different platforms, including Sanger sequencing, PacBio and Illumina sequencing, and is calculated empirically by using a data set with known accuracy.
B. Widely different, depending on the sequencing platforms, such as Sanger, PacBio, and Illumina
C. Impossible to calculate the Sanger sequencing platform
D. An indicator of the read quality, including background signal, ambiguities at nucleotide position, and strength of the signal. A higher Q score (e.g. 50) indicates very good quality of the DNA sequence called
E. A and D only
F. None of the above

E. A and D only

3

Which of the bellow steps is not uses in processing and analyzing NGS amplicon datasets?
A. Merge and quality trim reads
B. Align sequences and make a tree
C. Predict taxonomy (if applicable)
D. Remove potential chimeras
E. Further analyze sequences (alpha diversity, beta diversity, multivariate analysis)
F. Use a reference genome to assemble the reads into contiguous sequences (contigs)
G. Process sequences to get OTUs or ASVs
H. All of the above are used in processing amplicon NGS data

F. Use a reference genome to assemble the reads into contiguous sequences (contigs)

4

Match the following description to the proper diversity index.
Determining "species" diversity among different samples
A. alpha diversity
B. beta diversity

B. beta diversity

5

Match the following description to the proper diversity index.
Determining "species" diversity within a sample
A. alpha diversity
B. beta diversity

A. alpha diversity

6

The Cygwin program:
A. Is not a way to run native Linux apps on Windows
B. Is a collection of tools to provide a Linux look and feel environment for Windows machines
C. Is a DLL (dynamic link library) which acts as a Linux layer to provide substantial Linux functionality
D. All of the above
E. None of the above

D. All of the above

7

QUIIME and MOTHUR are
A. Both platforms are useful for analyzing sequence datasets from either Sanger or NGS sequencing platforms
B. Different in that QUIIME is a Python wrapping program; and MOTHUR is based on C++ programing
C. Both based on C++ programming
D. A and B only
E. None of the above

D. A and B only

8

The kmer methods of sequencing similarity comparison is...?
A. used to compare sequences in NGS datasets
B. based on alignments and phylogenetic trees
C. based on similarity of sequences in short (e.g. 4 or 6-nucleotide) stretches
D. A and C only
E. All of the above

D. A and C only

9

Match the "barcoding" gene with the proper group of organisms: Prokaryotes
A. rbcL (Rubisco gene)
B. mtCO1 (mitochondrial cytochrome oxidase 1)
C. 16S
D. 28S and 18S

C. 16S

10

Match the "barcoding" gene with the proper group of organisms: Plants
A. rbcL (Rubisco gene)
B. mtCO1 (mitochondrial cytochrome oxidase 1)
C. 16S
D. 28S and 18S

A. rbcL (Rubisco gene)

11

Match the "barcoding" gene with the proper group of organisms: Animals, often metazoa
A. rbcL (Rubisco gene)
B. mtCO1 (mitochondrial cytochrome oxidase 1)
C. 16S
D. 28S and 18S

B. mtCO1 (mitochondrial cytochrome oxidase 1)

12

Match the "barcoding" gene with the proper group of organisms: Eukaryotes in general
A. rbcL (Rubisco gene)
B. mtCO1 (mitochondrial cytochrome oxidase 1)
C. 16S
D. 28S and 18S

D. 28S and 18S

13

True or False?
Plats use small RNA to regulate expression of selected mRNAs in response to abiotic stresses, such as drought, prolonged cold winters, and nutrient deficiency

True

14

Who was the scientist who was an early evolutionist who proposed a theory that life forms could acquire information from their environment and pass it on in their genes? This proposal was ridiculous and dismissed.

John Baptise Lamarck (1744 -1829)

15

Which of the bellow is NOT a possible way to describe "epigenetics"?
A. A cellular memory, persistent homeostasis in the absence of the original perturbation pr an effect on cell fate not attributable to changes in DNA sequence.
B. Post-Transcriptional gene expression regulation processes
C. Post-Translational gene expression regulation processes.
D. Viability-quantitative PCR (v-qPCR) Microbial Source Tracking for the detecting of live bacteria
E. The process by which plants monitor environmental cues such as prolonged cold periods to adjust flowering activity
F. Phenotype plasticity

D. Viability-quantitative PCR (v-qPCR) Microbial Source Tracking for the detecting of live bacteria

16

Which of the below processes is not an "epigenetic" process?
A. Post-Transcriptional gene silencing
B. Pre-Transcriptional gene expression control through Heterochromatin DNA methylation
C. microRNA post-transcriptional gene silencing
D. small interfering RNA post-transcriptional gene silencing
E. Functional gene deep amplicon sequencing
F. Post-translational modification through histone acetylation
G. Post-translational modification through histone methylation

E. Functional gene deep amplicon sequencing

17

True or False?
MicroRNAs in one kingdom can repression gene expression or organisms in another (cross-kingdom miRNA expression regulation)

True

18

Binds the 3 prime untranslated region of the target transcript with imperfect complementarity. Usually this imperfect match to the target is in its "seed" region (nucleotides #2-8). The effect usually is suppression of target translation.

miRNA

19

Binds with PERFECT complementarity to its target, where it binds in the coding region. The effect of this binding results in a double-stranded RNA that is cleaved, resulting in target degradation.

siRNA

20

Cygwin basic commands on

slide 16 and 17

21

What are the ideal QS (quality score) and CRL (contiguous read length) scores for NGS?

QS of 40 or higher; CRL over 500

22

True or False? QIIME1 has more of a focus on ASVs than OTUs.

False (QIIME2 does)

23

Is the term barcoding used mainly by those who study prokaryotes or eukaryotes?

Eukaryotes

24

A motif (or small word) of length k observed more than once in a genomic or sequenced sequence

Kmer

25

Does the kmer method take more or less computational power than a sequence alignment?

Less!

26

What does Shannon diversity account for in alpha diversity estimation?

Abundance and evenness

27

Type of metagenomics where all of the different strains in a DNA mixture are fragmented (sheared) into small pieces. Adapters are added and NGS is performed. Uses sequence by synthesis.

Shotgun metagenomics

28

What is used to annotate the sequences produced in shotgun metagenomics?

MG-RAST

29

What is used to annotate the sequences produced in genomic sequencing (from pure culture)?

RAST or myRAST

30

During this step in data processing, you "call" Open Reading Frames (ORFs) and you may find groups of collectively expressed genes (e.g. operons in bacteria)

Annotation

31

During this step in data processing, sometimes a Reference Genome is used to "guide" the ordering of the short pieces into longer contiguous (CONTIGS) genome chunks

Assembly

32

During this step in data processing, HIGH Coverage is required to yield one chromosome (bacteria) and maybe plasmids if present

Complete Assembly

33

Sometimes called "supercontigs"

Scaffolds

34

Isothermal amplification is used in...

Cluster generation

35

What are two possible genome assemblers to use (with reference genome if available)?

Velvet or SPAdes

36

What software was used to assemble paired reads?

PEAR

37

What software was used to correct the assembly by comparing it to PEAR-assembled paired reads?

Pilon

38

What to program were used to check assembly quality?

QUAST and CheckM

39

Vernalization causes changes in what structure of the flowering repressor gene (FLC)?

Chromatic structure

40

Promotion of flowering after exposure to cold

Vernalization

41

Tissue-specific and developmental-stage-specific gene expression is often achieved through what modification?

Histone modification

42

What is another name for RNA interference (RNAi)?

Post Transcriptional Gene Silencing

43

Where was antisense RNA suppression first seen?

In petunias (pigment experiment)

44

What did the transgenic (chalcone synthase) petunias display?

Pigment gene cosuppresion

45

What kind of technology is commonly used as a molecular biology tool for in vivo and in vitro manipulations of gene expression?

Antisense RNA technology

46

Small interfering RNA with exact complementarity to "target" mRNA to be down regulated

siRNA

47

Which is used more commonly in plants, siRNA or miRNA?

siRNA

48

Which is used more commonly in animals, siRNA or miRNA?

miRNA

49

What is one mechanism by which stress induces virus production?

Alleviating miRNA-mediated repression of viral and/or host transcripts