Order ID:89JHGSJE83839 | Style:APA/MLA/Harvard/Chicago | Pages:5-10 |
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Sanger, Dideoxy Chain-Termination Sequencing
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Flag question: Question 1
Question 1 1 pts
Compared to so-called “Next-generation” or “Massively parallele” sequencing, what would be “First generation” sequencing?
Group of answer choices
a. Gel and/or capillary electrophoresis (CE) readout
b. PCR based sequencing methods of sequencing
c. Sanger, dideoxy chain-termination sequencing
d. Single molecule sequencing, for example with nanopores
Flag question: Question 2
Question 2 1 pts
What are key advantages of NGS compared to “First-generation” sequencing?
Group of answer choices
a. Reduced need for input sample (i.e. clone libraries)
b. Reduced need for size separation steps
c. Parallel readouts
d. All of the above
Flag question: Question 3
Question 3 1 pts
How do read lengths compare for Sanger vs NGS? This is a generalization, as newer technologies are improving things all the time
Group of answer choices
a. Sanger reads are usually shorter than NGS reads but the contigs are longer
b. Sanger reads are usually about the same as NGS reads
c. Sanger reads are usually longer than the most commonly encountered NGS reads
d. Sanger reads are rarely if ever longer than NGS, though the error profile is better
Flag question: Question 4
Question 4 1 pts
What factors make NGS faster and cheaper than Sanger sequencing?
Group of answer choices
a. Accuracy improvements streamline downstream processing
b. Shorter read lengths save time and money during sequencing and bioinformatics processing
c. Highly parallelized, smaller volumes, less input sample required
d. None of the above
Flag question: Question 5
Question 5 1 pts
Why are short reads problematic for some sequencing applications? This is a generalization, and “short” may be relative.
Group of answer choices
a. Short reads may be ambiguous with regard to overlap or genomic placement (i.e. “mapping”).
b. Short reads impact de novo assembly but not genotyping or sequencing per se
c. Short reads impact genotyping but not assembly or sequencing per se
d. Short reads primarily just increase error rates and therefore costs
Flag question: Question 6
Question 6 1 pts
Which best describes “mate-pairs” or “paired-end” reads
Group of answer choices
a. Shorter reads paired together to increase the total read length of your reaction.
b. Two reads separated by approximately known distance on a single starting DNA molecule.
c. Two reads taken together from the same sample DNA and arranged so as to span gaps.
d. Paired reads that align to form contigs then scaffolds, i.e. for genome assembly.
Flag question: Question 7
Question 7 1 pts
Which best describes “resequencing”?
Group of answer choices
a. Alignment of reads from one sample relative to a reference to identify variants.
b. Overlap of reads into contigs then scaffolds then an assembly.
c. Alignment of reads to find sequence features associated with phenotypes.
d. All of the above
Flag question: Question 8
Question 8 1 pts
Which best describes “de novo assembly”?
Group of answer choices
a. Alignment of reads from one sample relative to a reference to identify variants.
b. Overlap of reads into contigs then scaffolds then an assembly.
c. Alignment of reads to find sequence features associated with phenotypes.
d. All of the above
Flag question: Question 9
Question 9 3 pts
How does too-short read length impact common genomics applications? Specifically, how do short reads impact SNP genotyping and discovery? How do short reads impact assembly? Note “short” is a relevant term, but “too-short” implies functional limitations.
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Flag question: Question 10
Question 10 3 pts
How would you summarize the approach to sequencing advocated in the assigned paper (Aury JM, et. al. (2008) BMC Genomics, 9: 603. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies (Links to an external site.) )?
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RUBRIC |
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Excellent Quality 95-100%
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Introduction
45-41 points The background and significance of the problem and a clear statement of the research purpose is provided. The search history is mentioned. |
Literature Support 91-84 points The background and significance of the problem and a clear statement of the research purpose is provided. The search history is mentioned. |
Methodology 58-53 points Content is well-organized with headings for each slide and bulleted lists to group related material as needed. Use of font, color, graphics, effects, etc. to enhance readability and presentation content is excellent. Length requirements of 10 slides/pages or less is met. |
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Average Score 50-85% |
40-38 points More depth/detail for the background and significance is needed, or the research detail is not clear. No search history information is provided. |
83-76 points Review of relevant theoretical literature is evident, but there is little integration of studies into concepts related to problem. Review is partially focused and organized. Supporting and opposing research are included. Summary of information presented is included. Conclusion may not contain a biblical integration. |
52-49 points Content is somewhat organized, but no structure is apparent. The use of font, color, graphics, effects, etc. is occasionally detracting to the presentation content. Length requirements may not be met. |
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Poor Quality 0-45% |
37-1 points The background and/or significance are missing. No search history information is provided. |
75-1 points Review of relevant theoretical literature is evident, but there is no integration of studies into concepts related to problem. Review is partially focused and organized. Supporting and opposing research are not included in the summary of information presented. Conclusion does not contain a biblical integration. |
48-1 points There is no clear or logical organizational structure. No logical sequence is apparent. The use of font, color, graphics, effects etc. is often detracting to the presentation content. Length requirements may not be met |
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Sanger, Dideoxy Chain-Termination Sequencing