1. Sequencing Cyclic Peptides
Shayan Abtahi

2. What is the Problem?
Non ribosomal peptides can’t be found by looking for DNA region encoding it
Have to use mass spectrometer to sequence the peptide
Cyclic peptide so there are a lot of possibilities
Can’t realistically brute force
Noise in actual mass spectrometer data

3. How to Solve it
Score the theoretical spectrum of a peptide against experimental data
Algorithm maximizes the score of potential peptides
Input includes the number of potential peptides under consideration
Starts with generating potential peptides for each length and removing inconsistent ones
Starts with an empty peptide, and generates all potential 1-mers, then 2-mers etc… removing minimally scoring ones at each step

4. High level steps Expand function - generates list of k+1-mers
Trim function - Scores each peptide as if it were linear and retains the top N, where N is an input, scoring peptides

5. Results It worked Was ridiculously slow
So ridiculously slow I couldn’t actually finish checking tyrocidine B1 (VKLFPWFNQY) because my laptop is old garbage
But the output was correct until I had a memory error at around 9-mers