GeneDesigner

Overview

The IBG GeneDesigner is a component of the IBG Protein Desktop application which can be used to generate a DNA sequence from a given protein or amino acid sequnce that is optimized for protein expression and experimental manipulation. The application attempts to match codon frequency preference for the expression vector of the gene to ensure enhanced expression over random codon choice. Restriction enzyme sites can be requested for either inclusion or exclusion in the generated sequence. In addition, relative nucleotide frequency can be manipulated to prevent high GC content in the output sequence.

Functions

• organism codon preference matching
• restriction site manipulation
• nucleotide frequency shaping
• oligonucleotide generation **In progress**

Algorithm

The GeneDesigner uses a genetic algorithm to sample the large number of candidate sequences which are possible for a given amino acid sequence. Several of the GA parameters can be manipulated in the application:

• Mutation rate
• Crossover types **In progress**
• Population size
• Number of Generations
• Convergence factors **In progress**

Future work

As noted above, work on the GeneDesigner is in progress. We are currently finalizing the oligonucleotide generation algorithm and will be updating the graphical interface to simply the gene construction process. Future efforts will include a web-based version which uses the strength-Pareto algorithm for multiobjective optimization

Multi-objective optimization with EAs

• http://e-collection.ethbib.ethz.ch/ecol-pool/incoll/incoll_374.pdf
• http://ctr.stanford.edu/Summer00/sbalzarini.pdf
• DNA Sequence Optimization Using Constrained Multi-Objective Evolutionary Algorithm
• NACST/Seq: A Sequence Design System with Multiobjective Optimization

Paper being submitted to Computational Systems Bioinformatics Conference

• Revision 1.1 (incorporated feedback from Dave, Shohei, Jon, Kevin)
  • MS Word formatted
  • PDF
• Version submitted to CSB 2006
  • CSB_paper

-- RobVogelbacher - 26 Mar 2006