ProblemA2-1 - Computational Biology 03-310/311 & 42-334...

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Spring 2004 Problem A2 Robert F. Murphy Page 1 of 1 Problem A2 Finding coding sequences and PCR primers Due: February 3, 2004 Use MacVector to complete the following. Hand in requested printouts and written answers to the questions. Include justification for your answers (i.e., show basis of calculations). Reading MacVector User Guide, Chapter 11 Searching for Coding Regions MacVector User Guide, Chapter 10 Screening for Primers and Probes Questions (Total of 40 points) 1. Open the sequence pBR322 (it is in the Sample Files folder). Make a map of open reading frames (ORFs) using "universal" start and stop codons and print it. (b) Note that there are many ORFs of various sizes and that the feature map below the ORF map shows the locations of various known features of the sequence. Find the two largest ORFS (which correspond to the tet and bla genes). What reading frames are they in, and what nucleotides do they span?
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