hw2 - BCB 567/CprE 548 Bioinformatics I Fall 2007 Homework...

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Unformatted text preview: BCB 567/CprE 548 Bioinformatics I Fall 2007 Homework 2 Due Tuesday, September 25 1. (5 points) Given two sequences, which score is larger: their local alignment score or global alignment score? Why? How does their semi-global alignment score compare with the other two scores? 2. (5 points) Consider affine gap alignment with parameters ,,g, and h . Write an equation for the score of the best possible path that travels outside of the k- band for two strings of equal length n . 3. (5 points) Sequences generated by shotgun genome sequencing projects, called shotgun reads , can be thought of as 500-700 base pair sequences read from a random location on the genome of interest. Sometimes, foreign DNA sequence from a bacteria, called vector sequence , can contaminate the end of a shotgun read. Consider two shotgun reads A and B that have been read from overlapping locations on the genome. If it wasnt for the presence of the contaminating vector sequence, we would be able to find a high scoring suffix-prefix alignment...
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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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hw2 - BCB 567/CprE 548 Bioinformatics I Fall 2007 Homework...

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