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Abstract Detail



Poster Session

Wang, Qiong [1], Chai, Benli [1], Tiedje, James M. [2], Cole, James R. [1].

RDP: New tools for fungal analysis.

With the latest release, RDP (http://rdp.cme.msu.edu) includes a collection of fungal large subunit rRNA genes, and most RDP tools have been updated to work with this new fungal collection. This new set covers seven major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Blastocladiomycota, Zygomycota, Glomeromycota, and Neocallimastigomycota. The fungal training set for the RDP Classifier leverages a recently published phylogenetically consistent taxonomic mapping. The fungal alignment was created using the Infernal secondary-structure aware aligner trained on a hand-curated fungal rRNA structure model and full-length reference sequences, mostly from genome projects. The RDP Classifier, Hierarchy Browser, Sequence Match, Probe Match, and RDP Aligner, have all been updated to work with the new fungal 28S sequence collection. The new RDPipeline allows high-throughput analysis of fungal 28S rRNA amplicon data, as well as 16S bacterial and archaeal amplicon data. In addition we are currently evaluating fungal ITS1, 5.8S and ITS2 training sets for the RDP Classifier.   RDP FunGene (http://fungene.cme.msu.edu), RDP’s Functional Gene Pipeline and Repository, offers databases of common ecofunctional genes and proteins, many important for fungal community analysis, as well as integrated tools that allow researchers to browse these collections and use multiple filters to choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes. RDP’s mission includes user support; email rdpstaff@msu.edu or call +1(517)432-4997.


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Related Links:
Ribosomal Database Project
RDP Functional Database / Repository


1 - Michigan State University, Center for Microbial Ecology, 567 Wilson Rd - Rm 2225A, East Lansing, MI, 48824, USA
2 - Michigan State University, Center for Microbial Ecology, 1066 Bogue St, East Lansing, MI, 48824, USA

Keywords:
rRNA
phylogeny
classification
molecular phylogenetics.

Presentation Type: Offered Paper - Poster
Session: P1
Location: Lincoln Room/Kellogg Hotel and Conference Center
Date: Monday, June 9th, 2014
Time: 8:00 PM
Number: P1006
Abstract ID:131
Candidate for Awards:None


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