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Accueil > Français > Équipes > Génomique de l’environnement et bioinformatique (MEB) > Softwares


par DidierD - publié le , mis à jour le

PANAM : A Tool for the Phylogenetic Analysis and Taxonomic Affiliation of SSU rRNA Amplicons

The recent introduction of massively parallel pyrosequencing allows rapid, inexpensive taxonomic analysis of microbial communities from SSU rRNA amplicons. This growing flood of new data throws up a major challenge : that of accurately and rapidly building phylogenies and assigning a taxonomy to each experimental sequence. The vast datasets produced by pyrosequencers thwart standard phylogenetic techniques owing to limited computing resources and the need for manual curation. As a result, most of the methods dedicated to amplicon analyses, including their taxonomic assignment, are based on sequence similarity, and do not take into account the evolutionary information and putative environmental clades highlighted by phylogenetic methods.

We describe here a fully automated method named PANAM (Phylogenetic Analysis of Next-generation AMplicons) to annotate microbial SSU rRNA, with special emphasis on the analysis of microbial eukaryotic 18S rRNA, including both protists and unicellular fungi. PANAM, which is optimized to process large datasets, sorts experimental reads into different phyletic groups, processes ad hoc profile alignments and builds phylogenetic trees. Based on these trees, a taxonomy is assigned to each read, and reports of environmental clades and diversity estimators are generated. The results produced can therefore be used to analyze alpha diversity of communities or compare different communities (beta diversity).

PANAM can be used to analyze large datasets of SSU rRNA amplicons in a straightforward, automated procedure. It thus enables researchers to minimize those steps that require computing skills in the analysis of their data and instead focus on the biological interpretation of the results.

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