The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

Published online 7 November 2006 | J. R. Cole1,* , B. Chai1, R. J. Farris1, Q. Wang1, A. S. Kulam-Syed-Mohideen1, D. M. McGarrell1, A. M. Bandela1, E. Cardenas1, G. M. Garrity1,2 and J. M. Tiedje1,2
The Ribosomal Database Project (RDP-II) has introduced significant new features to enhance its capabilities in microbial ecology and related fields. Key updates include quality analysis, such as chimera detection, for all available rRNA sequences, and the introduction of myRDP Space, a web component that allows researchers to manage their own private sequence collections in sync with the RDP's public data. The project now maintains over 262,000 aligned and annotated rRNA sequences, with detailed updates from the International Nucleotide Sequence Database Collaboration (INSDC). All sequences are tested for anomalies using Pintail, and 21,771 sequences are flagged as anomalous. myRDP Space enables users to upload and align sequences, share data with Research Buddies, and access a high-throughput sequence processing pipeline tailored for single-read environmental sequence projects. Additional analysis services, such as the Hierarchy Browser, Sequence Match, RDP Classifier, Library Compare, and Tree Tool, have been enhanced to provide more robust tools for sequence analysis and microbial community comparison. The RDP-II website (http://rdp.cme.msu.edu/) offers detailed documentation and video tutorials to support users.The Ribosomal Database Project (RDP-II) has introduced significant new features to enhance its capabilities in microbial ecology and related fields. Key updates include quality analysis, such as chimera detection, for all available rRNA sequences, and the introduction of myRDP Space, a web component that allows researchers to manage their own private sequence collections in sync with the RDP's public data. The project now maintains over 262,000 aligned and annotated rRNA sequences, with detailed updates from the International Nucleotide Sequence Database Collaboration (INSDC). All sequences are tested for anomalies using Pintail, and 21,771 sequences are flagged as anomalous. myRDP Space enables users to upload and align sequences, share data with Research Buddies, and access a high-throughput sequence processing pipeline tailored for single-read environmental sequence projects. Additional analysis services, such as the Hierarchy Browser, Sequence Match, RDP Classifier, Library Compare, and Tree Tool, have been enhanced to provide more robust tools for sequence analysis and microbial community comparison. The RDP-II website (http://rdp.cme.msu.edu/) offers detailed documentation and video tutorials to support users.
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[slides and audio] The ribosomal database project (RDP-II)%3A introducing myRDP space and quality controlled public data