August Staubus Bio 131 Restriction Enzymes Cut DNA 160337 Seemingly Unrelated c engagecom r csborg Motif Discovered by looking at structures Thielking et al Data Downloaded all 160337 ID: 917264
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Slide1
Finding Motifs in Restriction Enzyme Sequences
August Staubus
Bio 131
Slide2Restriction Enzymes
Cut DNA
160,337
Seemingly Unrelated
c
engage.com
r
csb.org
Slide3Motif!
Discovered by looking at structures
Thielking
et al
Slide4Data
Downloaded all 160,337
Slide5High-Level Code
Choose the first k-
mer from the first protein sequence
Compute a profile for this k-merChoose the profile-most-probable k-mer from the next protein sequenceCompute a profile for the k-mers chosen so far
Compute the consensus of the selected k-mers
Compute the score of the selected k-mers
Repeat until the profile- most-probable
kmer
has been selected for each sequence
Ritz 2017
Ritz 2017
Slide6High-Level Code
Randomize the order of the protein sequences
Choose
the first a random k-mer from the first protein sequenceCompute a profile for this k-merChoose the profile-most-probable k-
mer from the next protein sequence
Compute a profile for the k-mers chosen so far
Compute the consensus of the selected k-mersCompute the score of the selected k-mers
based on amino acid mutation table
Repeat until the profile- most-probable
kmer
has been selected for each sequence
Ritz 2017
Repeat n times
Repeat
i
times
Slide7Results
Best 3-mer
Score
Best 2-mer
Score
Number of runs (
i
)
DLE
8
DE
5
25
AND
11
FR
5
50
RKG
12
HR
5
100
Slide83-mer↑ ↓2-mer