title: PROBEmer: A web-based software tool for selecting optimal DNA oligos.
abstract: 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.
authors.affiliation: Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA. semrich@iastate.edu
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Emrich
authors.forename: Mary
authors.initials: M
authors.lastname: Lowe
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics; D019295:Computational Biology; D017931:DNA Primers / Q000737:chemistry; D015342:DNA Probes / Q000737:chemistry*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D016681:Genome, Fungal; D020407:Internet; D015336:Molecular Probe Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015345:Oligonucleotide Probes / Q000737:chemistry*; D016366:Open Reading Frames; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers; D015342:DNA Probes; D015345:Oligonucleotide Probes; D012336:RNA, Ribosomal, 16S