ProblemSet1

ProblemSet1 - Introduction To Systems Biology Problem Set 1...

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Introduction To Systems Biology Problem Set 1 Please submit you answers with the code at the end of the document with a page break between the code for each program. Modular programs are encouraged (and you’ll probably find it easier), but are not required. In fact, that only strong requirement for the code portion of the assignment is that you comment your code well such that even a non-programmer would be able to follow what your program is doing. Answers should be uploaded to Blackboard and are due by the time of the next field trip. There’s not “right” way of doing many of these problems. The important thing is that you explain your methods, and describe how you dealt with any ambiguities that arose during your work. Questions? Lemme know (dag23@duke.edu). Good luck! 1) As we saw in class, the average 454 read is ~250 base pairs in length, and there are ~300,000 reads per run. The bacterium Escherichia coli (strain K-12) has a genome that is 4,639,000 base pairs long. How many runs on a 454 machine do you need to do to be 95% sure that each region of the genome is sequenced at least 10 times? How many runs do you need to do to sequence the human genome (3.3x10 9 base pairs in length) with similar coverage? You can solve this problem either analytically or by simulation. Show your work or include a copy of your code. 2) One type of repetitive DNA sequence seen frequently in the human genome is strings of a single base ( e.g. AAAAAA or TTTTTTT) known as homopolymers . Given what you know about pyrosequencing (the technology that lies behind 454 sequencing), why might homopolymers be difficult to sequence on a 454 machine? Why are homopolymers so much less of a problem for Solexa sequencing? 3) The program BLAST (which stands for Basic Local Alignment Search Tool) is one of
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ProblemSet1 - Introduction To Systems Biology Problem Set 1...

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