Endy:Notebook/DNA Sequence Refinement

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Project Description/Abstract



Use Cases, Requirements, Comments

  • Top Ten Needed Basic Parts (Parts Comprising the Central Dogma)
  1. Origins of DNA replication
    • Example: oriC
  2. Transcriptional Promoters
    • T7 ΓΈ10
  3. Transcriptional Operators
    • lambda oR
  4. RNA Processing Elements
    • An RNaseIII Site
  5. RNA Stability Elements
    • A Stemloop Hairpin
  6. Translational Start Sites
    • Ribosome Binding Sites
  7. Coding Sequences
    • Green Fluorescent Protein
  8. Translational Pause Sites
    • Regulation w/in the trp operon
  9. Translational Stop Sites
    • UAA
  10. Protein-Protein Interaction Epitopes
    • SH3 Domains
  • High-Level Problem Statement
    • A BioBrick standard specifies a set of restriction endonucleases that can be used for composing basic parts into composite parts
    • A non-standard DNA sequence is likely to have sites in the middle of the sequence that allow for the restriction enzymes specified in the standard to make a cut.
    • The algorithm has to identify those sites in the non-standard DNA sequence
    • The algorithm has to mutate the sites but must adhere to three constrains
      • The mutation eliminates the restriction site (the location where the restriction enzyme makes the cut)
      • The mutation does not change the amino acid that is suppose to be encoded if the sequence is an open reading frame
      • The mutation does not change the function of the sequence. For example, a mutation in a ribosome binding site (RBS) may lower or increase the affinity of the ribosome to the site




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