Exam1Key - CBio - Lesson 2 Course Teacher: Prof. Nir...

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BCB 444/544 Fall 2005 Exam 1 Key Friday, September 23 This closed-book, closed-notes 50-minute test consists of 7 questions. The number of points for each problem is indicated below. Read all questions carefully before starting. Write all your answers on the space provided in the exam paper. Remember that concise answers are preferable to wordy ones. Clearly state any simplifying assumptions you make in solving a problem. The last question is only for students enrolled in BCB 544. Name: 1 2 3 4 5 6 7 total 15 15 15 19 20 16 20 100 or 120
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1. (15 points) We saw three kinds of alignment in class: global, end-gap free, and local. Briefly explain when each type of alignment is the appropriate choice. Answer Global alignment is the appropriate choice when we already know that the sequences are related/similar. Since a global alignment tries to find the best alignment between the entire lengths of the sequence, it does not make a lot of sense to try to do a global alignment of two sequences that may not share any similarity. Local alignment is the correct choice when we don’t know anything about the poten- tial similarity between the sequences. Local alignment can detect similar portions of sequences without requiring the entire sequences to be similar. This is useful when the sequences are of different lengths, when you are searching for a shared domain or motif in proteins, or when you are aligning genomic DNA sequences to find similarity between conserved exons while ignoring the non-conserved introns. End-gap free alignment is a middle ground between global and local alignment. Gaps at the ends are not penalized, so we can have two sequences that only share similarity in a certain region. The most relevant biological example of when to use end-gap free
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This note was uploaded on 10/01/2009 for the course CS BCB/Co taught by Professor Olivereulenstein during the Fall '06 term at Iowa State.

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Exam1Key - CBio - Lesson 2 Course Teacher: Prof. Nir...

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