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OSP: a computer program for choosing PCR and DNA sequencing primers.

L Hillier1, P Green

  • 1Genetics Department, Washington University School of Medicine, St. Louis, Missouri 63110.

PCR Methods and Applications
|November 1, 1991
PubMed
Summary

The Oligonucleotide Selection Program (OSP) is a free tool that designs DNA primers for sequencing and PCR. It successfully selects primers by screening for potential base-pairing issues and user-defined parameters.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Primer selection is critical for DNA sequencing and PCR success.
  • Nonspecific priming and secondary structures can hinder amplification and sequencing accuracy.
  • Existing methods may lack comprehensive screening for potential primer-associated issues.

Purpose of the Study:

  • To introduce the Oligonucleotide Selection Program (OSP) for automated primer design.
  • To provide a tool that minimizes nonspecific priming and secondary structures.
  • To offer customizable constraints for primer and product characteristics.

Main Methods:

  • OSP screens candidate oligonucleotide primers against various sequences including self-pairing, primer-dimers, and product sequences.
  • User-defined parameters include length, G+C content, melting temperature, and 3' end stability.

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  • A combined score, based on weighted user-defined parameters, ranks primer candidates.

    • Main Results:

    • OSP successfully selects sequencing primers for the *C. elegans* genome with >96% success.
    • OSP selects human genomic PCR primer pairs with an 81% success rate.
    • The program screens for base-pairing at primer 3' ends and internal sequences separately.

    Conclusions:

    • OSP is an effective and extensively used tool for designing DNA primers for large-scale sequencing and PCR projects.
    • The program's comprehensive screening and customizable parameters contribute to high primer selection success rates.
    • OSP is freely available for research purposes in both text and graphical versions.