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Unformatted text preview: CMSC 423: Project #2: Finding Several Good Local Alignments Due: Tuesday, December 8th at 11:59pm. In this second project, you will implement local alignment with a ffi ne gaps along with a scheme for finding several good alignments, not just the best. The project will be done in groups of 2 these groups can be di erent from those in part 1. Some of your grade for the project will be based on a confidential survey completed by your partner. Format of the command: Your program will be run using the following command: java multilocal.jar score.matrix in.fasta out.fasta k where k is an integer that gives the desired number of alignments. Your program must compile on the submit server. It should output into out.fasta the k best local alignments of the two sequences in in.fasta (see below). Format of input: The format of the score.matrix file will be the same as in Project #1. The format of the in.fasta file is the same as in Project #1 as well, except that it can contain only 2 sequences. Youfile is the same as in Project #1 as well, except that it can contain only 2 sequences....
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- Fall '07