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Bern Slides

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Douda Samih
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15 views7 pages

Bern Slides

Uploaded by

Douda Samih
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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RECREATING THE

PAM250 MATRIX
MIRIAM BERN
THE PROBLEM

• PAM 250 Matrix used to score sequence alignments


• Provides more accurate understanding of which amino acids
will be conserved and which mutations will occur
• Is it easy to replicate?
• Anna’s DNA example:
Why was it not symmetric?
HOW DID I SOLVE IT?

• Turned steps of Dayhoff paper into Python code


• Wrote functions to compute the PAM250 Matrix from the
Accepted Point Mutations Matrix
• Used the steps to replicate Anna’s DNA example to see what
went wrong
DATA
• Started out with the Accepted Point Mutations Matrix from the
paper as a text file
• Made Python dictionaries from the relative mutabilites and
frequencies listed in the paper
• Used the equations in the paper to construct the matrices
• Checked program output against the matrices in the paper
HIGH LEVEL STEPS

• Step 1: Calculate proportionality constant (lambda)


• Step 2: Using the Accepted Point Mutations Matrix, relative mutabilities,
and lambda, create Mutation Probability Matrix for 1 PAM
• Step 3: Using Python package NumPy, multiply the matrix by itself 250
times to get the Mutation Probability Matrix for 250 PAMs
• Step 4: Divide by the frequency to get the Relatedness Odds Matrix
• Step 5: Take the log of these values to get the Log Odds Matrix
• Step 6: Reorder the Log Odds Matrix to match the amino acid order in the
paper and cut it in half
RESULTS: PAM250

• I got the same answers! (With a few rounding errors)


RESULTS: CLASS EXAMPLE

• Question: Why was the class example asymmetric?


• No proportionality constant used in DNA example
• Definitions of frequency and relative mutability make it
unlikely that nucleotides with different mutabilities would
appear the same number of times

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