Oligonucleotide Probe Design for Large Genomes using Multiple Spaced Seeds

Abstract

<p>An oligonucleotide is a small fragment of DNA or RNA that is designed to hybridize with a unique piece in a target sequence. Oligonucleotides have a wide range of applications in molecular biology and medicine. They can be used as probes to screen for diseases and viral infections in medicine as well as DNA microarray design, polymerase chain reaction (PCR) amplication, and gene identication in molecular biology.</p> <p>The major computational challenge for designing oligonucleotide probes is finding the optimal probe for each target sequence. Each probe must be specific to its target sequence, must be sensitive in order to detect the target sequence, and the set of oligonucleotides must be uniform under the same experimental conditions. Many algorithms and software programs have been created for this problem, however, none is able to solve it very well.</p> <p>We introduce a new method for oligonucleotide design that employs sensitive multiple spaced seeds, and show that our algorithm computes unique and more efficient oligonucleotides as well as executing orders of magnitude faster than the other algorithms that have been proposed for the same task.</p>