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MAPD: a probe design suite for multiplex ligation-dependent probe amplification assays.

Jizu Zhi1

  • 1Bioinformatics Core Facility, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA. jzhi@ic.sunysb.edu.

BMC Research Notes
|May 25, 2010
PubMed
Summary

The MAPD software now simplifies probe design for methylation-specific MLPA (MS-MLPA) and supports mouse and rat genomes, improving DNA copy number variation analysis.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Multiplex ligation-dependent probe amplification (MLPA) is a cost-effective technique for DNA copy number variation (CNV) analysis.
  • MLPA is widely used in research and diagnostics, bridging genome-wide and single-gene analyses.
  • Probe design for MLPA, especially for new applications like MS-MLPA and non-human genomes, remains challenging.

Purpose of the Study:

  • To enhance the H-MAPD software with new features for MLPA probe design.
  • To address the challenges in probe selection for MS-MLPA and other genomes.
  • To provide a user-friendly tool for the MLPA community.

Main Methods:

  • The study describes updates to the H-MAPD software, now referred to as MAPD.
  • New features include probe selection algorithms for MS-MLPA and support for mouse and rat genomes.

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  • A physical-chemical property verification tool for user-defined probes was implemented.

    • Main Results:

    • The enhanced MAPD software offers improved probe selection for MS-MLPA.
    • Support for mouse and rat genomes expands the applicability of MLPA analysis.
    • The inclusion of new stuffer sequences and a verification tool streamlines probe design.

    Conclusions:

    • MAPD is a free, web-based tool designed to facilitate MLPA probe design.
    • The previous version, H-MAPD, had approximately 200 users globally.
    • The new features aim to increase convenience and efficiency for MLPA users worldwide.