prelab quiz 7 Flashcards
Order the following steps (or procedures) required to produce a phylogenetic tree using samples from unknown animal tissues (you must give the correct order to receive full credit, no partial credit)
PCR Purification
BLAST software
PHYLIP software
MUSCLE software
Extraction of DNA from animal sample
DNA sequencing
Amplification barcoding gene
__3__ PCR Purification
__5__ BLAST software
__7__ PHYLIP software
__6__ MUSCLE software
__1__ Extraction of DNA from animal sample
__4__ DNA sequencing
__2__ Amplification barcoding gene
The DNA sequencing software measures the fluorescence emitted in each of four channels – A, T, C, G – and records these as a trace, or electropherogram. What is the name of the software program that analyzes the sequence file and “calls” a nucleotide (A, T, C, G) for each peak?
BLAST
Pubmed
Phred
MUSCLE
Phred
If two or more nucleotides have relatively strong signals at the same position, what does the software do?
it calls an “N” for an undetermined nucleotide
It randomly chooses the strongest signal
it calls an “N” for No nucleotide
It reads the signal a second time
it calls an “N” for an undetermined nucleotide
The software also examines the peaks around each call and assigns a quality score for each nucleotide. What does the quality score measure? (Select all that apply)
the length of the sequence
the number of Ns in the sequence
the probability that each nucleotide call is wrong
the accuracy of each call
the probability that each nucleotide call is wrong
the accuracy of each cell
What is the error rate and accuracy associated with a quality score of 20? (select all that apply)
Accuracy of 80%
Error rate of 20%
Error rate of 1 in 100
Accuracy of 99%
Accuracy of 90%
Error rate of 1 in 10
Accuracy of 80%
Error rate of 20%
Error rate of 1 in 100
Accuracy of 90%
Error rate of 1 in 10
What is the meaning of the term “BLAST”
Best Local Alignment Silver Tool
Basic Line Algorithm Search Tool
Basic Local Alignment Search Tool
Bank of Lengthy Accession Sequence Tool
Basic Local Alignment Search Tool
In this experiment, what is the purpose of doing a BLAST search?
We can identify the unknown species based on sequence
comparison
We can determine the sequence of the unknown sample
We can determine if the sequences are good quality
We can compare the sequences of the PTC gene
We can identify the unknown species based on sequence
comparison
What is MUSCLE?
software tool that searches an unknown sequence against all existing sequenced genomes
software tool that trims unaligned ends of DNA sequences
software tool that provides links to detailed descriptions of different species
software tool that aligns several DNA sequences
software tool that aligns several DNA sequences
Why is MUSCLE necessary for building a phylogeny?
The alignments will always reveal the most common ancestors
MUSLCE provides morphological evidence that two species are related
The sequence alignments reveal proteins required to infer relationships between different species
Alignment of DNA sequences can reveal SNPs between different sequences and infer evolutionary relationships
Alignment of DNA sequences can reveal SNPs between different sequences and infer evolutionary relationships
