CBB/CPSC Programming Assignment #2: GOR
CBB/CPSC Programming Assignment #2: GOR
Background:
Predicting the secondary structure of proteins based on their amino acid sequence is an arduous task. Therefore, various methods have been proposed to address this issue. The GOR method is a commonly used algorithm to predict the secondary structure of proteins. This procedure is founded on well-established principles such as information theory and Bayesian statistics. GOR IV is an improved version of the original GOR method and uses all possible pairs within a window to predict the secondary structure of the amino acid located in the center of the window.
Assignment:
The second programming assignment is to implement GOR IV using a window size of 17 in which all possible pairs of amino acids are used to predict the secondary structure of the central amino acid. The program must be implemented in Python. The usage of NumPy (NumPy is package for scientific computing with Python) is allowed, but not required.
A training data set and testing data set of protein sequences and their associated secondary structures can be found at . The training data set (n = 1,000) is used to calculate the log scores. Subsequently, these log scores are utilized to predict the secondary structure of the proteins in the testing data set (n = 20). An overall prediction accuracy should be calculated. Note that the prediction of the first and last eight amino acids for each protein sequence is optional (boundary condition).
Suggested output format:
Sequence 1:
PDSVIKQMQKDTGMGAWNLYAALYGTQ
ECHCCCCHHCCCCCCHHHHEHHHHCCC
Legend: H (alpha-helix), E (beta-sheet), C (coil)
Submission:
1) Source code
2) README file with instructions how to run your program
3) Test run of your implementation
Assignments should be e-mailed to cbb752@.
DUE DATE: February 25, 2009 by 5 PM.
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