Apr 19, 2024  
2020-2021 Undergraduate Academic Catalog 
    
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2020-2021 Undergraduate Academic Catalog [ARCHIVED CATALOG]

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EB 3430 - Bioinformatics II

2 lecture hours 2 lab hours 3 credits
Course Description
This course introduces students to the practical application of currently available bioinformatics tools to various real world problems including comparative analysis of homologous biological sequences to address evolutionary/phylogenetic relationships between a wide variety of different organisms, 3D visualization of large complex biological macromolecules, cross-analysis of biological sequences and their corresponding 3D structures to identify and characterize various redundant sequence and structural motifs essential in defining both the higher order 3D architecture and the cellular function of many biologically active macromolecules, and molecular modeling to predict the 3D structure of biologically important macromolecules whose higher-order structure is not available yet. (prereq: EB 3420 )
Course Learning Outcomes
Upon successful completion of this course, the student will be able to:
  • Search, collect, and align homologous biological sequences of interest
  • Create a quality alignment of biological sequences
  • Build and interpret a phylogenetic tree based on well-aligned biological sequences
  • Derive sequence-structure relationships by comparing biological sequences and their structure data
  • Compare the 3D structures of homologous biomolecules
  • Visualize and appreciate the detailed 3D structures of very complex biomolecules using various molecular visualization tools
  • Identify and characterize various sequence and structural motifs from a detailed cross-analysis of biological sequences and their corresponding higher-order 3D structures
  • Perform homology modeling to predict the 3D structure of a biological sequence whose structure is not yet available
Prerequisites by Topic
  • None 
Course Topics
  • RNA sequence analysis
  • The Tree of Life: phylogenetic relationships between organisms
  • Sequence-Structure relationships of biological macromolecules
  • 3D structure of protein and RNA
  • 3D visualization of biomolecular structures and their analysis
  • Sequence and structural motifs in biological macromolecules
  • Homology modeling of novel biological macromolecules
Laboratory Topics
  • Comparative analysis of RNA sequences (2 labs)
  • The Tree of Life and phylogenetic analysis (2 labs)
  • Sequence-structure relationships of biomolecules (1 lab)
  • Comparative analysis of 3D protein and RNA structures (1 lab)
  • 3D visualization and analysis of biomolecular structure (1 lab)
  • Sequence and structural motifs in biomolecules (1 lab)
  • Homology molecular modeling (1 lab)
Coordinator
Dr. Jung Lee


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