Lecture 8-9 questions

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

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Unformatted text preview: CSE182 Lecture 8,9 questions Vineet Bafna October 23, 2006 The questions are open ended, but should help you understand lectures better. Do these questions make sense? Are they helpful in following the lecture? Constructive feedback is appreciated. 1. Recall that we use a geometric method to distinguish coding versus non-coding. (L8, Slides 11,12). This method relies upon computing the angles α, β between two vectors. How do we compute the angles between two vectors? 2. Suppose you find a candidate sequence for which the E-score given by α α + β is 0 . 4. How can you increase your confidence in your prediction? 3. Define the problem of computational gene finding? What is a transcript? What is UTR? What are donor and acceptor sites? 4. Suppose you are given the entire cDNA transcript of a human gene. You are also told that the first intron contains a special regulatory site. Describe an algorithm to get the first intron assuming that the donor site begins with GT, and acceptor site ends with AG.site begins with GT, and acceptor site ends with AG....
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