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Digital Logic for Medicine and Biology Research: A hardware implementation of the Smith-Waterman algorithm for DNA comparison

Author: Dr. Javier Resano

In this project, students learn that the comparison of DNA sequences is important to a wide variety of applications in medicine and biology, including the analyses of ecosystem biodiversity, cancer mutations and the evolution of viruses. The students learn that specialized yet inexpensive digital hardware based on field programmable gate arrays can help speed the analysis of DNA sequences. They design and test a simple implementation of the Smith-Waterman algorithm that is broadly used for DNA sequence comparisons. In the process, they learn about computational platforms, digital logic, and a divide-and-conquer approach to design.

Download All Files 3.155 MB*
Background Lecture:Background Lecture (960.625 KB)
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Student Project Assignment*:Student Project Assignment* (72.031 KB)
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Faculty Project Description:Faculty Project Description (154.981 KB)
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Project Report Solution*:Project Report Solution* (138.116 KB)
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Summary Lecture:Summary Lecture (167.044 KB)
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Additional Project Materials*:Additional Project Materials* (1.158 MB)
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Additional Project Materials*:Additional Project Materials* (181.545 KB)
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Additional Project Materials*:Additional Project Materials* (1.001 MB)


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