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Updated: Jun 27, 2026

Multiplex PCR and Reverse Line Blot Hybridization Assay (mPCR/RLB)
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ProSeeK: a web server for MLPA probe design.

Lorena Pantano1, Lluís Armengol, Sergi Villatoro

  • 1Genes and Disease Program, Center for Genomic Regulation (CRG), Doctor Aiguader, Catalonia, Spain. lorena.pantano@crg.es

BMC Genomics
|December 2, 2008
PubMed
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We developed ProSeeK, a web tool that optimizes custom probe design for Multiplex Ligation-dependent Probe Amplification (MLPA) assays. This tool significantly reduces the time and effort required for designing probes, aiding in copy number variation studies.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genome-wide copy number variations (CNVs) are increasingly recognized as significant contributors to human diversity and disease susceptibility.
  • Multiplex Ligation-dependent Probe Amplification (MLPA) is a targeted method for assessing CNVs at up to 40 genomic loci simultaneously.
  • Custom MLPA assay design, while common, presents challenges in the time-consuming oligonucleotide probe design process.

Purpose of the Study:

  • To develop a computational tool to streamline and optimize the design of custom oligonucleotide probes for MLPA assays.
  • To reduce the turnaround time and improve the efficiency of custom MLPA assay development.

Main Methods:

  • Development of a web-based tool utilizing a custom algorithm for probe design.

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  • The algorithm accepts target sequences in FASTA format and user-defined parameters specific to MLPA assays.
  • Identification of optimal probes within a given genomic region based on specified criteria.

    • Main Results:

    • A novel web tool, ProSeeK, has been created to facilitate and optimize custom probe design for MLPA experiments.
    • The tool efficiently identifies the best probes by processing target sequences and user-defined parameters.
    • The algorithm significantly reduces the time required for probe design.

    Conclusions:

    • ProSeeK is the first tool available for optimizing custom probe design in MLPA assays.
    • The tool's ease of use and speed dramatically decrease the time needed for probe design.
    • ProSeeK is expected to be a valuable resource for laboratories conducting copy number variation studies using MLPA.