Paper Info
Title
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
Abstract
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.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.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/.
Year
DOI
Venue
2006
10.1186/1471-2105-7-7
BMC Bioinformatics
Keywords
Field
DocType
software validation,genetics,bioinformatics,expressed sequence tag,sequence alignment,algorithms,microarrays,expressed sequence tags
Software tool,Sequence alignment,Expressed sequence tag,Biology,UniGene,Oligonucleotide,Software,Bioinformatics,Software verification and validation,Genetics,DNA microarray
Journal
Volume
Issue
ISSN
7
1
1471-2105
Citations 
PageRank 
References 
47
1.27
11
Authors
6
Name
Order
Citations
PageRank
Jie Zheng11508.54
Jan T Svensson2532.51
Kavitha Madishetty3471.27
Timothy J. Close4989.74
Tao Jiang51809155.32
Stefano Lonardi62940175.19