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Nucleic Acids Research, 2003, Vol. 31, No. 13 3746-3750
© 2003 Oxford University Press

PROBEmer: a web-based software tool for selecting optimal DNA oligos

Scott J. Emrich*,1,2,4, Mary Lowe3 and Arthur L. Delcher4,5

1 Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA 2 Biology Department, Loyola College in Maryland, Rockville, MD, USA 3 Physics Department, Loyola College in Maryland, Rockville, MD, USA 4 Computer Science Department, Loyola College in Maryland, Rockville, MD, USA 5 The Institute for Genomic Research, Rockville, MD, USA

*To whom correspondence should be addressed. Tel: +1 515 294 3811; Fax: +1 515 294 8432; Email: semrich{at}iastate.edu

PROBEmer (http://probemer.cs.loyola.edu) is a web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. The software has been used to obtain genus-specific prokaryotic probes based on the 16S rRNA gene, gene-specific probes for expression analyses and PCR primers. In this paper, we describe how to use PROBEmer, the computational methods it employs, and experimental results for oligos identified by this software tool.


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