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

Scott J Emrich1, Mary Lowe, Arthur L Delcher

  • 1Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA. semrich@iastate.edu

Nucleic Acids Research
|June 26, 2003
PubMed
Summary
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PROBEmer is a web tool for selecting optimal oligonucleotide (oligo) probes for PCR and multiplex arrays. It identifies specific oligo sequences for target nucleic acids while avoiding non-target sequences, preventing cross-hybridization.

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Selecting specific oligonucleotide (oligo) probes is crucial for PCR and various molecular detection platforms.
  • Existing methods may lack efficiency in identifying probes that are both specific to target sequences and absent from non-target sequences, leading to potential cross-hybridization issues.

Purpose of the Study:

  • To introduce PROBEmer, a web-based software tool designed for selecting optimal oligonucleotide probes.
  • To describe the computational methods employed by PROBEmer for identifying specific probes and predicting cross-hybridization.
  • To present experimental validation of probes identified using PROBEmer.

Main Methods:

  • PROBEmer utilizes a comparative approach, analyzing target and non-target nucleic acid sequence groups.

Related Experiment Videos

  • The software identifies oligo sequences present in the target group but absent from the non-target group.
  • Near-neighbor analysis is performed on non-target sequences to predict and display potential cross-hybridization alignments.

    • Main Results:

    • PROBEmer successfully identified genus-specific prokaryotic probes using the 16S rRNA gene.
    • The tool was effective in designing gene-specific probes for expression analyses.
    • Experimental results confirmed the utility of oligos identified by PROBEmer for various applications, including PCR primers.

    Conclusions:

    • PROBEmer provides a robust computational solution for designing specific oligonucleotide probes.
    • The software aids in minimizing cross-hybridization, enhancing the reliability of molecular assays.
    • PROBEmer is a valuable tool for researchers in molecular biology, genomics, and bioinformatics.