Classifier - Start

Introduction

new Classifier now provides gene copy number adjustment for 16S gene sequences. The 16S gene copy number data is provided by rrnDB website.

new We are pleased to release two new Fungal ITS training sets to classify fungal ITS sequences. Warcup is an version from an active curatorial effort kindly provided by Paul Greenfield, Vinita Deshpande and colleagues of the Australian CSIRO [V. Deshpande et al. 2015. Fungal identification using a Bayesian Classifier and the 'Warcup' training set of Internal Transcribed Spacer sequences. Mycologia (108(1): 1-5. doi:10.3852/14-293]. UNITE is a set consisting of UNITE core sequences for each dynamic species hypothesis provided by Kessy Abarenkov of UNITE. See RDP's technical report Comparison of Three Fugal ITS Reference Sets for detailed analysis. The Warcup V2 release notes is released in June 2016.

How to cite Classifier? Wang, Q, G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol. 73(16):5261-7. The RDP Classifier publication has been selected by Essential Science Indicators as the most-cited paper in a highlighted research area of microbiology. It's featured in December 2011 Science Watch.

NOTE: The classifier requires a sequence with at least 50 bases to get a good classification result. The number of query sequences can be submitted online is limited to 100000. For larger dataset, use the command-line version available as part of RDPTools package from github.com/rdpstaff or SourceForge.

Help topics: Partial sequences with length shorter than 250 bps should use bootstrap cutoff 50%.


Please enter your sequences:

Running Jobs: 0; Pending Jobs: 0

Choose a gene:


Did you know you can select sequences from myRDP and Hierarchy Browser to do classification?

Choose a file (unaligned format) to upload:


Cut and paste sequence(s) (in Fasta, GenBank, or EMBL format):
   

 

Questions/comments: rdpstaff@msu.edu
Creative Commons License: Attribution-ShareAlike

 Move to Toptop topMove to Top