Data Mining Algorithms with Pseudoknot Free Codes
Abstract
Synthetic DNA is proposed for use as an information storage media and three-dimensional structural material in nanotechnology. The main requirement of these systems is large collections of oligonucleotides that will not crosshybridize. The process of designing them has come to be known as DNA word, or DNA code, design. In this research, the DNA code generating software, SysDCode was developed and refined to include pseudoknot secondary structure, simulate hybridization assays, and applied to DNA hybridization algorithms. SynDCode has the ability to create new DNA codes with high binding specificity, filter existing codes through verification, and extend codes where specific oligonucleotides are essential to overall system construction. SynDCode's robust yet efficient computational model allows for the exploration of unparalleled search space spawning superior codes with higher binding specificity.
Document Details
- Document Type
- Technical Report
- Publication Date
- May 01, 2006
- Accession Number
- ADA453576
Entities
People
- Anthony Macula
- Morgan Bishop