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Assignment 4

# An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

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Biological Data Analysis (CSE 182) : Assignment 4 Logistics Submit a hard copy containing the code and results. Create a compressed ﬁle containing the code and output as separate ﬁles, and email Julio. Do not deviate signiﬁcantly from the suggested ﬁle names. The assignment is due by 12/7, midnight. Computational Mass Spectrometry 1. (25 pts.) Compute the Isotope Pattern of the peptide SLAMMER. Submit a plot of the the ﬁrst 4 peaks, as well as your calculations. Assume the following: The peptide has charge = 1. The height of the highest peak is 100 (Note: we only care about the relative heights). Only two isotopes are important C - 13, with abundance 2%, and O - 18, with abundance 5%. Note that these abundances are given for illustration purposes. In reality, the natural abundance of isotopes is smaller. 2. (25 pts.) Mass spectra are often written in a simple text format, such as .dta. An example of a tandem mass spectrum S 1 in (.dta format) for an unknown peptide P is given on the web-site.
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Unformatted text preview: (a) Describe the format of the ﬁle S 1 in words. What is the parent mass and charge of P ? (Note: Use the web to understand the .dta format.) (b) Identify the peptides in S 1 and S 2 using Mascot MS/MS ion search (http://www.matrixscience.com/search form select.html). Note that S 2 is a diﬃcult example, so please use caution. Once the peptide is ’identiﬁed’, give your own reasons for the identiﬁcation being correct. Such reasons could include percentage of b-y ions matched, percentatge of total intensity explained, and so on. 3. (48pts.) Design and implement an algorithm perf which takes as input a binary character matrix, and constructs a perfect phylogeny if one exists. The output of the program should be a tree (described as a set of parent child relationships). Test your algorithm on the two data-sets provided. 4. (2pts.) What language did you use? How much time did you take to do the assignment? Who did you discuss your homework with?...
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