Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Oligospawn: A Software Tool For The Design Of Overgo Probes From Large UniGene Datasets

Jie Zheng¹ , Jan T. Svensson² , Timothy J. Close² , Tao Jiang¹ , Stefano Lonardi¹

¹  Department of Computer Science & Engineering, University of California, Riverside, CA 92521, USA

²  Department of Botany & Plant Sciences, University of California, Riverside, CA 92521, USA

Backgroud: Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets.
Result: OligoSpawn is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but dose not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. We will demonstrate the functionalities of OligoSpawn.
Conclusion: The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of serveral tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OligoSpawn is freely available at http://oligospawn.ucr.edu/.