CSCI 5481 (001, 771, 881) Computational Techniques for Genomics (Fall 2021)

CSCI 5481 (001, 771, 881) Computational Techniques for Genomics (Fall 2021)

Course Modules

Introduction and fundamentals of molecular biology

Introduction and fundamentals of molecular biology
Module Completed Module In Progress Module Locked
Introduction and fundamentals of molecular biology 969067  
  • Page
    Class Overview (Video) Class Overview (Video)
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  • Page
    Basics of Human Genome (Video) Basics of Human Genome (Video)
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  • Attachment
    Elements of Biology.pdf Elements of Biology.pdf
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  • Context Module Sub Header

    Readings: Chpt 1-3

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  • External Url
    Animation of Central Dogma Animation of Central Dogma
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  • External Url
    Genome Browser Genome Browser
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  • External Url
    Protein Databank Protein Databank
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  • External Url
    GenBank GenBank
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Sequence Alignment

Sequence Alignment
Module Completed Module In Progress Module Locked
Sequence Alignment 978786  
  • Attachment
    Sequence Alignment.pdf (Updated new slides 9/27) Sequence Alignment.pdf (Updated new slides 9/27)
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  • Page
    Sequence Alignment (Video) Sequence Alignment (Video)
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  • Context Module Sub Header

    Readings: Chpt 4-5

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  • External Url
    How to compute PAM matrix How to compute PAM matrix
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  • External Url
    Sequence alignment with matlab Sequence alignment with matlab
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  • External Url
    NCBI BLAST/PSI-BLAST NCBI BLAST/PSI-BLAST
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Hidden Markov Models

Hidden Markov Models
Module Completed Module In Progress Module Locked
Hidden Markov Models 982549  
  • Attachment
    HMMs.pdf (Updated 10/7) HMMs.pdf (Updated 10/7)
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  • Page
    HMMs (Video) HMMs (Video)
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  • Attachment
    MSA.pdf MSA.pdf
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  • External Url
    Profile HMMs (Video of Lecture on 10/13) Profile HMMs (Video of Lecture on 10/13)
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  • Context Module Sub Header

    Readings: Chpt 6

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  • External Url
    Easygene (HMM for gene finding prokaryotes) Easygene (HMM for gene finding prokaryotes)
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  • External Url
    pfam pfam
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Phylogeny

Phylogeny
Module Completed Module In Progress Module Locked
Phylogeny 988668  
  • Attachment
    Phylogeny.pdf (Updated 10/29) Phylogeny.pdf (Updated 10/29)
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  • External Url
    Lecture (10/19) Lecture (10/19)
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  • Page
    Lecture Video (10/27) Lecture Video (10/27)
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  • Context Module Sub Header

    Readings: Chpt 7 and 8

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Large-scale DNA Sequencing

Large-scale DNA Sequencing
Module Completed Module In Progress Module Locked
Large-scale DNA Sequencing 993165  
  • Page
    NGS video and De Bruijn Graph video NGS video and De Bruijn Graph video
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    Readings

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  • External Url
    Nature focus on NGS Nature focus on NGS
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  • External Url
    NGS Review NGS Review
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  • Attachment
    SRC-RR-124.pdf SRC-RR-124.pdf
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  • Attachment
    bowtie.pdf bowtie.pdf
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  • Attachment
    BWA.pdf BWA.pdf
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Protein Structures and Functions

Protein Structures and Functions
Module Completed Module In Progress Module Locked
Protein Structures and Functions 997125  
  • Attachment
    Protein structure and function.pdf Protein structure and function.pdf
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  • Page
    Protein Structure and Function; Protein Classification (Video) Protein Structure and Function; Protein Classification (Video)
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  • Attachment
    ProteinClassification.pdf ProteinClassification.pdf
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  • Context Module Sub Header

    Readings: Chpt 11-14

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Genome Annotation

Genome Annotation
Module Completed Module In Progress Module Locked
Genome Annotation 1005752  
  • Attachment
    Genome Annotation.pdf Genome Annotation.pdf
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  • Page
    Genome Annotation (Video) Genome Annotation (Video)
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  • Context Module Sub Header

    Readings: Chpt 9 & 10

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Useful resources:

Useful resources:
Module Completed Module In Progress Module Locked
Useful resources: 966519  
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    Programming resources:

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    Matlab

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  • External Url
    Obtain Matlab (current release: R2021a) Obtain Matlab (current release: R2021a)
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  • Page
    Matlab installation Matlab installation
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  • External Url
    Matlab bioinformatics toolbox Matlab bioinformatics toolbox
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  • Context Module Sub Header

    Python

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    Obtain Python (Version 3.8) Obtain Python (Version 3.8)
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  • Page
    Python installation Python installation
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  • External Url
    Python bioinformatics package (Biopython) Python bioinformatics package (Biopython)
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    Teaching staff:

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  • Context Module Sub Header

    Instructor: Rui Kuang (kuang@umn.edu)

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  • Context Module Sub Header

    TA: Yoshitaka Inoue (inoue019@umn.edu)

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Office hours

Office hours
Module Completed Module In Progress Module Locked
Office hours 977012  
  • External Url
    Prof. Kuang's office hours on Zoom: 1pm-2pm Tuesdays; additional hours 1:45pm-2pm Fridays will be added before assignments due Prof. Kuang's office hours on Zoom: 1pm-2pm Tuesdays; additional hours 1:45pm-2pm Fridays will be added before assignments due
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  • External Url
    TA Yoshitaka Inoue's office hour (Zoom): 2pm-3pm Fridays TA Yoshitaka Inoue's office hour (Zoom): 2pm-3pm Fridays
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minimum score must view must submit must contribute