Endy:Notebook/DNA Sequence Refinement

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Developers

 * Alexander Castro
 * Drew Endy
 * Cesar Rodriguez

Use Cases, Requirements, Comments

 * Top Ten Needed Basic Parts (Parts Comprising the Central Dogma)
 * 1) Origins of DNA replication
 * 2) *Example: oriC
 * 3) Transcriptional Promoters
 * 4) *T7 ø10
 * 5) Transcriptional Operators
 * 6) *lambda oR
 * 7) RNA Processing Elements
 * 8) *An RNaseIII Site
 * 9) RNA Stability Elements
 * 10) *A Stemloop Hairpin
 * 11) Translational Start Sites
 * 12) *Ribosome Binding Sites
 * 13) Coding Sequences
 * 14) *Green Fluorescent Protein
 * 15) Translational Pause Sites
 * 16) *Regulation w/in the trp operon
 * 17) Translational Stop Sites
 * 18) *UAA
 * 19) Protein-Protein Interaction Epitopes
 * 20) *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

Algorithms

 * Algorithm Proposal I
 * Developer: Alexander Castro

Source Code

 * Google Code Site