OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
BACKGROUND
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.


RESULTS
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 does 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. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it.


CONCLUSIONS
The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several 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/.
Zheng
Jie
J
Department of Computer Science & Engineering, University of California, Riverside, CA 92521, USA. zjie@cs.ucr.edu
Svensson
Jan T
JT
Madishetty
Kavitha
K
Close
Timothy J
TJ
Jiang
Tao
T
Lonardi
Stefano
S
D001483:Base Sequence; D030541:Databases, Genetic; D004867:Equipment Design; D019544:Equipment Failure Analysis; D020224:Expressed Sequence Tags; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D015345:Oligonucleotide Probes; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D012986:Software Validation
D015345:Oligonucleotide Probes