BCB/CprE/ComS 548 Fundamental Algorithms in Computational Biology Fall 2005 Homework 1 Due Monday, September 13 1. (5 points) Find the best local alignments between the two sequences AGGCAT and GTGCTGC . Use the following scoring system: 10 for a match,-5 for a mismatch and-5 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.zool.iastate.edu/aat/align/align.html which provides 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. Try the default parameter values. Next, use the parameters: mismatch penalty = 10, gap opening penalty = 0, gap extension penalty = 5; Then, use the same
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