CS Grade Server (grades.cs.umd.edu)
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Date |
Topics |
Slides/Lecture notes |
Add'l resources |
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08/30 |
Introduction |
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09/04 |
Molecular biology primer Programming for Bioinformatics |
www.bioperl.org |
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09/06 |
Bioinformatics Databases |
Homework 1 due |
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09/11 |
Sequence alignment - global |
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09/13 |
Sequence alignment - local |
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09/18 |
Intro to NGS Sequencing and Assembly |
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09/20 |
Genome Assembly |
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09/25 |
Suffix arrays Data compression |
Lecture 8 |
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09/29 |
Suffix trees/arrays & midterm recap |
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10/01 |
Midterm 1 |
basic biology + exact matching |
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10/06 |
Sequence alignment - inexact matching |
Inexact
alignment Dr. Pop out of town |
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10/08 |
Midterm recap |
Alignment heuristics Chap. 6 |
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10/13 |
Sequence alignment - inexact matching |
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10/15 |
Sequence alignment - inexact matching, affine gaps |
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10/20 |
Sequence alignment heuristics Chaining algorithms |
Project part 2 due |
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10/22 |
Multiple sequence alignment Motif finding |
Chap. 6.7 |
ClustalW |
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10/27 |
Genome sequence assembly |
Genome
assembly |
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10/29 |
Genome sequence assembly |
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11/03 |
Phylogenetic trees Tree analysis/display |
Chapter 12 Project part 3 due |
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11/05 |
Midterm 2 |
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11/10 |
Phylogenetic analysis |
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11/12 |
Genetic association studies |
Chap. 13 |
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11/17 |
Genetic association studies |
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11/19 |
"Signal" finding Hidden Markov Models |
not in book |
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11/24 |
Data clustering |
Chap. 11.1-11.6 |
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11/26 |
Thanksgiving |
no class |
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12/01 |
RNA structure prediction |
not in book |
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12/03 |
What you missed... |
Final project due!!! |
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12/08 |
Recap |
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12/10 |
Recap/Review |
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12/14 |
Final exam |
CSIC 1121, 8-10am |
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