Final Exam Flashcards
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.
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
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)
Match the following description to the proper diversity index.
Determining “species” diversity among different samples
A. alpha diversity
B. beta diversity
B. beta diversity
Match the following description to the proper diversity index.
Determining “species” diversity within a sample
A. alpha diversity
B. beta diversity
A. alpha diversity
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
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
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
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
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)
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)
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
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
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)
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
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
True or False?
MicroRNAs in one kingdom can repression gene expression or organisms in another (cross-kingdom miRNA expression regulation)
True
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
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
