MIT 6 047 - Problem Set #1 (3 pages)

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Problem Set #1



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Problem Set #1

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Lecture Notes


Pages:
3
School:
Massachusetts Institute of Technology
Course:
6 047 - Computational Biology

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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 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 NeedlemanWunsch 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 ll in the score and traceback matrices The skeleton program speci es 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 y The fruit y 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 b Make minor adjustments to your alignment program so that the score it computes can be interpreted



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