Sequencing Antibiotics using Bioinformatics

  1. Partitioning the strand into “codons”: non overlapping sets of three consecutive bases.
  2. Matching each codon with it’s respective amino acid based on the genetic code.
  1. We can’t do so by making use of a genome because these proteins do not correlate to DNA.
  2. Most NRPs are cyclic — so rather than being coded for in a linear fashion which have one obvious start and end, there are instead multiple possible “starts” and “ends”.
  1. expands the list of existing leaderboard peptides by creating a version with each of the possible letters tacked on to the end. Ex the peptide “GA” would be replaced by “GAG”, “GAE”, “GAD”…etc. This is the branching step.
  2. gets rid of the peptides whose mass is larger than the Parent Mass. This is the bounding step.
  3. For each peptide whose mass is equal to the parent mass, it compares it’s theoretical linear spectrum to the spectrum in question. If they are equal, we save the peptide, or else we discard it.
  1. compute the convolution.
  2. choose the M most frequent elements to form the alphabet of amino acids which we will use for expansion.
  3. run the previously defined branch and bound leaderboard cyclopeptide sequencing algorithm using this algorithm.

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Avery Parkinson

Avery Parkinson

Activator at The Knowledge Society | A Sandwich or Two Founder