Assignment Goals

  • Solve a fundamental problem in computational biology.

  • Learn about strings in C.

  • Learn about the analysis of algorithms.

    • Checking Your Work and Hints

  • Various test protein and genetic input files are located at /u/cs126/files/sequence/.

  • You may use our reference solution sequence126 to test your solution.

  • Here's a link to some hints if you need a place to get started.

    • Submission and readme
  • Submit the following files: 
    readme.txt sequence.c

  • The readme.txt file should contain the following information. Here is a template readme file.

  • Name, precept number, high level description of code, any problems encountered, and whatever help (if any) your received.

  • A table of running times (in seconds) for the input files listed.

  • An estimate of the running time and memory consumption as a function of N, where N is the number of characters in the input file.

  • Your submitted program should handle strings of length up to 10,000. It's fine to declare a global 10,001 x 10,001 array and use only the part of it that you need. Caution: if you are running on a Windows system and get an error message like 
    
The system cannot execute the specified program.
    then use a smaller value, say 9001 x 9001, when testing, but your submitted code should still use 10,001 x 10,001.

    • Enrichment Links
    The genetic data are taken from the National Center For Biotechnology Information. This site also contains many examples of such database and alignment software.

    Kevin Wayne