RISA Aligner Environmental Microbial Genomics Group

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RisaAligner software to align fluorescent data between Agilent 2100 Bioanalyzer chips

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. The comparison of fingerprints actually relies upon the precise estimation of all amplified DNA fragment lengths. However, size standard computation can vary between gel runs. Moreover, for complex samples such as soil microbial communities, DNA fragment length corresponding to intergenic spacer sizes is sometimes limited to discriminating between samples, whereas comparison of whole fluorescence data (electrophoregrams) can be more accurate. However, when more than one chip is involved, electrophoregram comparisons are challenging due to the unavoidable discrepancies between chips and the absence of correction by the Agilent software when not working with DNA sizing. This paper presents RisaAligner software developed for analyzing and comparing electrophoregrams from Agilent chips by using a non-linear ladder-alignment algorithm. We demonstrate the robustness and the substantial improvements in data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.

The software risaAligner is a free software under license Apache 2.0 (http://www.apache.org/licenses/LICE...). The software risaAligner is developed in JAVA, and can be downloaded hereafter:

Zip - 8.9 Mb

So as to execute risaAligner on your computer you must have a recent version of JAVA, which can be downloaded for free at https://www.java.com/fr/download/.
There is nothing to install: just download the file risa-aligner.zip, unpack it and start (= double click) the program risaAligner.jar.

IMPORTANT REMARK: you must unzip the whole file (unzipping the only file risaAligner.jar will not work).

In case of problems, you can contact: riccardo.scorretti[at]ec-lyon.fr

Publications

Elisabeth Navarro, Olivier Fabrègue, Riccardo Scorretti, Jérémy Reboulet, Pascal Simonet, Lorna Dawson and Sandrine Demanèche. 2015. RisaAligner software to align fluorescent data between Agilent 2100 Bioanalyzer chips;application to soil microbial community analysis.

 Corresponding author :sandrine.demaneche@ec-lyon.fr

 

 

   

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