Suppose you were using paired-end sequencing with 250 cycles. How much of the genome of a...
Suppose you were using paired-end sequencing with 250 cycles. How much of the genome of a stickleback fish would you expect to sequence at >7X coverage if you used EcoRI/MspI?
Homework Answers
One can cover almost the entire genome of stickleback fish as ECoR1 occurs 1/46= 1 in 4096 no sequence as it is 6 bp cutter. MsP1 on the other hand is a 4bp cutter and occurs in 1/44 bp. Thus one would cover most of the regions of the genome when coverage is 7x. Though there will be several centromeric repeats paired sequencing can give considerable degree of coverage . Assembly of the sequences will be consuming time. At greater than 7x coverage one will obtain more than 90% of the genome
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Suppose you were using paired-end sequencing with 250 cycles.
How much of the genome of a...
Question 4 Part A [10 marks] A human genome has been re-sequenced using a sequencing technology that produces 100 bp reads of high quality data. The DNA was sheared to make a paired-end library with...
Question 4 Part A [10 marks] A human genome has been re-sequenced using a sequencing technology that produces 100 bp reads of high quality data. The DNA was sheared to make a paired-end library with a size range of 1500 bp +- 500 bp and sequenced to generate paired-end reads. The analysis pipeline takes short-read sequence data and aligns it to a repeat-masked version of the reference human genome sequence assembly using BLASTN. This table summarizes the results from three...
A-E please 10. You inherit a sequencing machine and decide to sequence the genome of an...
A-E please
10. You inherit a sequencing machine and decide to sequence the genome of an animal. A. (2pts) What animal would you pick? Briefly explain why. B. (6pts) How would you find the protein-coding genes in a new genome sequence? Describe one computational method and one experimental method. C. (4pts) List 4 other DNA elements would you expect to find in a new genome in addition to protein-coding genes? D. (3pts) If you compared the chromosomal organization of dogs,...
Assume you are working to sequence the genome of a newly identified alien species. The alien...
Assume you are working to sequence the genome of a newly identified alien species. The alien DNA is composed of the same nucleotides are in us and, its genome is 2-3 times larger than that of any terrestrial organism, and this genome is contained within 2 huge linear chromosomes and once smaller circular chromosome. Assume , mechanisms of biology (i.e. transcription, translation, replication, etc. are similar to those acting in terrestrial eukaryotes. That said, here is no reason to believe...
Illumina Sequencing short answer questions A. Suppose that there was a mistake and the nucleotides you...
Illumina Sequencing short answer questions A. Suppose that there was a mistake and the nucleotides you ordered for sequencing were all labeled with blue tags. How would this affect the results? Explain your reasoning. B. When template is added to the flow cell for bridge PCR, the concentration of template is critical. What would happen if too many template molecules were added to the flow cell?
Questions 9-12 deal with SSR loci in Sam's genome. Remember that SSRs (simple sequence repeats) are...
Questions 9-12 deal with SSR loci in Sam's genome. Remember that SSRs (simple sequence repeats) are tandem (next to each other) repeats of short sequences (a few bp). Such tandem repeats are located at specific sites scattered throughout the genome. Individuals vary in the number of repeats at each site sites can have up to 100 repeats. Each locus with the same repeats is called an SSR ocus DNA was extracted from Sam's white blood cells and cut with a...
Generally, describe how the sequencing data was analyzed for differential gene expression. How was it determined...
Generally, describe how the sequencing data was analyzed for differential gene expression. How was it determined that genes were differentially expressed using DESeq? 2. 3. At the end of the DESeq pipeline, you got a list of 1000 differentially expressed genes. Which command would have changed the number of differentially expressed genes? How would it have done so?
How much is $250 to be received in exactly one year worth to you today if...
How much is $250 to be received in exactly one year worth to you today if the interest rate is 12%? The value today is $? (Round your response to the nearest penny) This same $250 received in one year would be worth ______ to you today if the interest rate rose to 17% More , less, the same amount.
Suppose that Earth were moved to a distance of 2 AU from the Sun. How much...
Suppose that Earth were moved to a distance of 2 AU from the Sun. How much stronger or weaker would the Sun's gravitational pull be on the Earth? Explain.
Suppose that you were interested in investigating the effect of a drug that is to be used in the treatment of patients who have glaucoma in both eyes. A comparison between the mean reduction in eye pressure for this drug and for a standard treatment is de
Suppose that you were interested in investigating the effect of a drug that is to be used in the treatment of patients who have glaucoma in both eyes. A comparison between the mean reduction in eye pressure for this drug and for a standard treatment is desired. Both treatments are applied directly to the eye.a. Describe how you would go about collecting data for your investigation.b. Does your method result in paired data? Explain.c. Can you think of a reasonable...
How would your initial answer for Sau3A change if you knew that the average GC content of the human genome was 35%? Express your answer using three significant figures. fragments Submit Previous Answ...
How would your initial answer for Sau3A change if you knew that the average GC content of the human genome was 35%? Express your answer using three significant figures. fragments Submit Previous Answers Request Answer X Incorrect: Try Again; 4 attempts remaining Part F How would your initial answer for BamHI change if you knew that the average GC content of the human genome was 35%? Express your answer using three significant figures. fragments
How would your initial answer for...
Question 4 Part A [10 marks] A human genome has been re-sequenced using a sequencing technology that produces 100 bp reads of high quality data. The DNA was sheared to make a paired-end library with a size range of 1500 bp +- 500 bp and sequenced to generate paired-end reads. The analysis pipeline takes short-read sequence data and aligns it to a repeat-masked version of the reference human genome sequence assembly using BLASTN. This table summarizes the results from three...
A-E please
10. You inherit a sequencing machine and decide to sequence the genome of an animal. A. (2pts) What animal would you pick? Briefly explain why. B. (6pts) How would you find the protein-coding genes in a new genome sequence? Describe one computational method and one experimental method. C. (4pts) List 4 other DNA elements would you expect to find in a new genome in addition to protein-coding genes? D. (3pts) If you compared the chromosomal organization of dogs,...
Questions 9-12 deal with SSR loci in Sam's genome. Remember that SSRs (simple sequence repeats) are tandem (next to each other) repeats of short sequences (a few bp). Such tandem repeats are located at specific sites scattered throughout the genome. Individuals vary in the number of repeats at each site sites can have up to 100 repeats. Each locus with the same repeats is called an SSR ocus DNA was extracted from Sam's white blood cells and cut with a...
Generally, describe how the sequencing data was analyzed for differential gene expression. How was it determined that genes were differentially expressed using DESeq? 2. 3. At the end of the DESeq pipeline, you got a list of 1000 differentially expressed genes. Which command would have changed the number of differentially expressed genes? How would it have done so?
How would your initial answer for Sau3A change if you knew that the average GC content of the human genome was 35%? Express your answer using three significant figures. fragments Submit Previous Answers Request Answer X Incorrect: Try Again; 4 attempts remaining Part F How would your initial answer for BamHI change if you knew that the average GC content of the human genome was 35%? Express your answer using three significant figures. fragments
How would your initial answer for...
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