Simulated sequencing by hybridization using evolutionary programming

Sequencing of DNA is among the most important tasks in molecular biology. DNA chips are considered to be a more rapid alternative to more common gel-based methods of sequencing. Previously, we demonstrated the reconstruction of DNA sequence information from a simulated DNA chip using evolutionary programming. The research presented here extends this work by relaxing several assumptions adopted in our initial investigation. We also examine the relationship between base composition of the target sequence and the useful set of probes required to decipher the target on a DNA chip. Comments regarding the nature of the optimal ratio for the target and probe lengths are offered. Our results go further to suggest that evolutionary computation is well-suited to address the sequence reconstruction problem.