Master Thesis Defense - Scott Schoeller

Friday, April 9, 2021
10:00 AM - 11:00 AM
Event Type
Computer Science
Contact
Roberts, Sue M
Link
https://mastercal.uww.edu/MasterCalendar/EventDetails.aspx?EventDetailId=40704

Title: A Simple, Space-Efficient Algorithm for Detecting Start and Stop Codons in DNA 

Via webex: 

https://uww.webex.com/uww/j.php?MTID=mf8941e8bf26ed17fc307d1d36592bcdc

Abstract: The brute force algorithm for string matching has a worst-case execution complexity of O(MN), where N is the length of the entire string and M is the length of the substring to be matched. The efficiency of brute-force matching is insufficient for biological applications due to the sheer size of bioinformatics datasets.

This thesis describes an algorithm that uses bit compression techniques to represent multiple codons in a single Python integer. It was proven that with exact matching steps, the search algorithm is as accurate as brute-force matching with significantly higher efficiency, as this algorithm runs in O(N) time and space, with minimal memory overhead. While the bit-based algorithm is not more space-efficient in a theoretical sense, it is more efficient practically as we have observed significant memory savings compared to the size of the original string.

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