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Updated: Mar 29, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
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RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil

Elisabeth Navarro1,2, Olivier Fabrègue1, Riccardo Scorretti1

  • 1Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.

Biotechniques
|December 15, 2015
PubMed
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Ribosomal Intergenic Spacer Analysis (RISA) software, RisaAligner, enables accurate microbial community comparison using electrophoregrams. This addresses challenges in analyzing complex soil samples with Agilent Bioanalyzer data.

Area of Science:

  • Microbiology
  • Bioinformatics
  • Molecular Ecology

Background:

  • Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution technique for microbial community fingerprinting.
  • Visualizing RISA profiles with the Agilent 2100 Bioanalyzer is common, but fragment size estimation can vary.
  • Comparing complex microbial communities, like soil samples, using fragment size alone is often insufficient.

Purpose of the Study:

  • To develop a robust method for analyzing and comparing RISA electrophoregrams from Agilent chips.
  • To address experimental variations and lack of software correction when comparing multiple chips.
  • To improve the analysis of complex soil microbial community profiles.

Main Methods:

  • Development of RisaAligner software utilizing a nonlinear ladder-alignment algorithm.
Keywords:
RISA comparisonalignment toolmicrobial ecology

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  • Analysis and comparison of electrophoregrams generated from Agilent DNA 1000 and High Sensitivity chips.
  • Application to soil microbial community profiling.

    • Main Results:

    • RisaAligner software demonstrates robustness in analyzing and comparing RISA electrophoregrams.
    • Significant improvement in data analysis accuracy for soil microbial communities.
    • Effective handling of experimental variations between Agilent chips.

    Conclusions:

    • RisaAligner provides a reliable solution for comparing RISA data across multiple Agilent chips.
    • The software enhances the discriminatory power for complex microbial communities.
    • This approach offers a substantial improvement for microbial ecology studies using RISA.