Deciphering Molecular Evolution (Bioinformatics IV)

开始时间: 04/22/2022 持续时间: Unknown

所在平台: CourseraArchive

课程类别: 其他类别

大学或机构: University of California, San Diego （加州大学圣地亚哥分校）

课程主页: https://www.coursera.org/course/molecularevolution

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课程详情

Two landmark bioinformatics-related discoveries made headlines in 2003.

First, the deadly Severe Acute Respiratory Syndrome (SARS) virus caused panic as it swept around the globe in a few weeks. But where did SARS come from? By constructing an evolutionary tree of the unknown virus as well as viruses taken from other species, we can not only understand which animal gave us SARS, but also reconstruct its path around the globe. This is just one of many problems in modern biology related to constructing evolutionary trees.

Second, a team of biologists announced that some proteins had miraculously survived within a 68 million year old dinosaur fossil. Moreover, they concluded that the amino acid sequences of these dinosaur proteins were nearly identical to sequences in modern-day chickensl. Based on this discovery, famed paleontologist Jack Horner (who partly inspired the character of Dr. Grant from Jurassic Park) hopes to resurrect dinosaurs by genetically re-engineering a chicken. But did these peptides really come from T. rex, or do they represent statistical artifacts or contamination? To answer this question, we will need to explore the field of computational proteomics.

课程大纲

Which Animal Gave Us SARS? (Evolutionary Tree Reconstruction)

The Fastest Outbreak
Transforming Distance Matrices into Evolutionary Trees
Toward An Algorithm for Distance-Based Phylogeny Construction
Additive Phylogeny
Using Least Squares to Construct Approximate Distance-Based Phylogenies
Ultrametric Evolutionary Trees
The Neighbor-Joining Algorithm
Character-Based Tree Reconstruction
The Small Parsimony Problem
The Large Parsimony Problem
Epilogue: Evolutionary Trees Fight Crime

Was T. rex Just a Big Chicken? (Computational Proteomics)

Paleontology Meets Computing
What Proteins Are Present in This Sample?
Decoding an Ideal Spectrum
From Ideal to Real Spectra
Peptide Sequencing
Peptide Identification
Peptide Identification Meets the Infinite Monkey Theorem
Spectral Dictionaries
T. rex Peptides: Treasure Trove of Ancient Proteins or Artifact of Contamination?
Epilogue: From Unmodified to Modified Peptides

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课程简介

In this course, we will see how evolutionary trees resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans. We will then use methods from computational proteomics to test whether we can reconstruct Tyrannosaurus rex proteins and prove that birds have evolved from dinosaurs.