Assignment 2

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

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Biological Data Analysis (CSE 182) : Assignment 2 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 Ng. Do not deviate significantly from the suggested file names. Late submission will incur a penalty of 10pts for every day that the assignment is late . Sequence Alignment and Gap penalties 1. (40 pts.) Implement a space-efficient program locAL to align two long DNA sequences with linear gap-penalty. The program should take two DNA sequences as input, along with user defined values for match-score , mismatch-score , indel . Its should be invoked as follows: locAL <seq file1> <seq file2> -m <match> -s <mismatch> -d <indel> and should output the following: Score of the best local-alignment. Length of the best local-alignment The alignment itself. Apply the program to aligning the two pairs of sequences (available on the course web-site) with the following parameters: match:1, mismatch -30, indel -20. Submit the code, and the output.
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This homework help was uploaded on 02/14/2008 for the course CSE 182 taught by Professor Bafna during the Fall '06 term at UCSD.

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Assignment 2 - Biological Data Analysis (CSE 182) :...

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