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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 file 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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