title: RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.
abstract: Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.
authors.affiliation: Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.|IRD-UMR LSTM, Campus de Baillarguet, Montpellier, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Navarro
authors.affiliation: Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Fabrègue
authors.affiliation: Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Scorretti
authors.affiliation: Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.
authors.forename: Jérémy
authors.initials: J
authors.lastname: Reboulet
authors.affiliation: Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Simonet
authors.affiliation: James Hutton Institute, Aberdeen, UK.
authors.forename: Lorna
authors.initials: L
authors.lastname: Dawson
authors.affiliation: Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Demanèche
mesh_terms: D000465:Algorithms; D016172:DNA Fingerprinting / Q000379:methods*; D021901:DNA, Intergenic / Q000737:chemistry*; D017711:Nonlinear Dynamics; D025341:Principal Component Analysis; D012984:Software; D012988:Soil Microbiology
chemical_list: D021901:DNA, Intergenic
keywords: RISA comparison; alignment tool; microbial ecology