Uncovering Motifs in Restriction Enzyme Sequences and Protein Structures
Explore the discovery of motifs in restriction enzyme sequences and protein structures, analyze high-level code for motif identification, and uncover results from motif scoring experiments. Dive into the world of bioinformatics with valuable insights provided in this comprehensive study.
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Presentation Transcript
Finding Motifs in Restriction Enzyme Sequences August Staubus Bio 131
Restriction Enzymes Cut DNA 160,337 Seemingly Unrelated cengage.com rcsb.org
Motif! Discovered by looking at structures Thielking et al
Data Downloaded all 160,337
High-Level Code Choose the first k-mer from the first protein sequence Compute a profile for this k-mer Choose 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- mers Compute the score of the selected k-mers Ritz 2017 Repeat until the profile- most- probable kmer has been selected for each sequence Ritz 2017
High-Level Code Randomize the order of the protein sequences Choose the first a random k-mer from the first protein sequence Compute a profile for this k-mer Choose 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- mers Compute 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 Repeat n timesRepeat i times Ritz 2017
Results 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
3-mer 2-mer
