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MIT6_047f08_pset01

MIT6_047f08_pset01 - MIT OpenCourseWare http/ocw.mit.edu...

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MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms .
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6.047/6.878 Fall 2007 Problem Set 1 Due: Monday September 15 at 8pm 1. Evolutionary distance and whole-genome duplication . In this problem, you will implement the Needleman- Wunsch algorithm for pairwise sequence alignment, apply it to the protein-coding sequences of related genes from several mammalian genomes, and use the results to learn about their evolution. (a) On the class web site, we have provided a skeleton program ps1-seqalign.py , which you will com- plete. We provide a traceback routine, but you will write the code to fill in the score and traceback matrices. The skeleton program specifies a substitution matrix and gap penalty. If you so choose, you may rewrite the program in any programming language. Please submit (1) the portion of the code that you wrote; (2) an optimal alignment the two sequences AGGTGAT and AGTAA , and corresponding score matrix F with the optimal path indicated; and (3) the score of the alignment of the human and mouse HoxA13 genes, which we also provide on the web site. The Hox cluster is a set of genes that are crucial in determining body plan formation during embryo development. They are found in all bilateral animals, in species as distant as the fruit fly. The fruit fly has one Hox cluster, while most vertebrates have four. It is thought that vertebrates have undergone two rounds of whole-genome duplication, giving rise to four Hox clusters from the ancestral one. In the remainder of this problem, you will use your Needleman-Wunsch alignment program to analyze the sequences of several Hox genes, and estimate the date of the most recent vertebrate whole-genome duplication. In particular, we are interested in using the N-W alignment score as a distance metric between two sequences.
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