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

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...

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Bibliographic Details
Published in:Nucleic acids research 2003-07, Vol.31 (13), p.3746-3750
Main Authors: Emrich, Scott J., Lowe, Mary, Delcher, Arthur L.
Format: Article
Language:English
Subjects:
Algorithms
Bacteria - genetics
Computational Biology
Databases, Genetic
DNA Primers - chemistry
DNA Probes - chemistry
Gene Expression Profiling - methods
Genome, Fungal
Internet
Molecular Probe Techniques
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Probes - chemistry
Open Reading Frames
Polymerase Chain Reaction - methods
RNA, Ribosomal, 16S - genetics
Saccharomyces cerevisiae - genetics
Sequence Analysis, DNA - methods
Software
User-Computer Interface
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Summary: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.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkg569