hw1 - BCB/CprE/ComS 548 Fundamental Algorithms in...

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BCB/CprE/ComS 548 Fundamental Algorithms in Computational Biology Fall 2007 Homework 1 Due Tuesday, September 11 1. (5 points) Find the best local alignment(s) between the two sequences AGCCAT and GTGCCTGA . Use the following scoring system: 4 for a match, 3 for a mismatch and 2 for a gap. 2. (5 points) The purpose of this problem is to experiment with sequence alignment software. Point your browser to the URL http://deepc2.psi.iastate.edu/aat/align/align.html which pro- vides a variety of alignment software (developed by ISU professor Xiaoqiu Huang). The interface uses the FASTA format, in which a sequence such as AGGCAT is represented as >name AGGCAT where the sequence name is optional. Run the global alignment program GAP and local alignment program SIM on the two E. Coli genomic sequences from the text ±le accompanying the homework (found on the course web under “homeworks homework 1 supplement”). Try the default parameter values. Next, use the parameters: mismatch penalty = 10, gap
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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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hw1 - BCB/CprE/ComS 548 Fundamental Algorithms in...

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