Practical Bioinformatics Mark Voorhies 5/21/2019 Mark Voorhies - - PowerPoint PPT Presentation

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Oct 31, 2022 139 likes •264 views

Practical Bioinformatics Mark Voorhies 5/21/2019 Mark Voorhies Practical Bioinformatics Change of Coordinates http://xkcd.com/123/ Mark Voorhies Practical Bioinformatics Principal Components Analysis (PCA) Is there a point of view that

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Practical Bioinformatics

Mark Voorhies 5/21/2019

Mark Voorhies Practical Bioinformatics

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Change of Coordinates

http://xkcd.com/123/ Mark Voorhies Practical Bioinformatics

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Principal Components Analysis (PCA)

Is there a point of view that makes our data easier to look at?

Mark Voorhies Practical Bioinformatics

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x′ = ax + by + cz y′ = dx + ey + fz z′ = gx + hy + iz   x′ y′ z′   =   a b c d e f g h i     x y z  

Mark Voorhies Practical Bioinformatics

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Principal Components Analysis (PCA)

Is there a point of view that makes our data easier to look at?

Mark Voorhies Practical Bioinformatics

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Principal Components Analysis (PCA)

Is there a point of view that makes our data easier to look at? Implemented as Singular Value Decomposition (SVD) after centering (covariance PCA) and, possibly, scaling (correlation PCA)

Mark Voorhies Practical Bioinformatics

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Correlations among more than two samples

Y X

Mark Voorhies Practical Bioinformatics

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Correlations among more than two samples

Y X Y X

Mark Voorhies Practical Bioinformatics

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Correlations among more than two samples

Y X Y X Y X Z

Mark Voorhies Practical Bioinformatics

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Correlations among more than two samples

Y X Y X Y X Z Y X Z

Mark Voorhies Practical Bioinformatics

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Homework: Dictionaries

1 Write a function to return the antisense strand of a DNA

sequence in 3’→5’ orientation.

2 Write a function to return the complement of a DNA

sequence in 5’→3’ orientation.

3 Write a function to translate a DNA sequence Mark Voorhies Practical Bioinformatics