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Lab4 - CSci 3003 Introduction to Computing in Biology Lab...

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CSci 3003: Introduction to Computing in Biology Lab Assignment #4 30 points Assigned: 2/10/10 Due: 2/23/10 (before midnight) Goals of this lab: Practice manipulating arrays. Become familiar with using conditional statements and loops. Practice reading in data from files, doing analysis, producing output. Practice using hashes. Part I: Analysis of ORF (open reading frame) length of yeast genes (1) Download a file containing all yeast genes and their chromosomal coordinates here: http://www-users.itlabs.umn.edu/classes/Spring-2010/csci3003/files/lab4/yeast_orflist.txt Open the file and look at how it’s formatted. (2) Write a script that does the following: a. Opens the file for reading and reads in the data b. Prints the name of the shortest and longest gene. Briefly describe what’s known about the functions of these genes? (HINT: you might find http://yeastgenome.org helpful for investigating the functions of the genes) c. Creates two output files, one called yeast_crickstrand_genes.txt and one called yeast_watsonstrand_genes.txt. Print out a list of genes that are encoded on the Crick strand to first file and genes that are encoded on the Watson strand to the second file. (HINT: the last letter in the ORF name, either W or C, tells you which strand the gene is encoded on) d. Compute and print the mean ORF length.
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