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June 15, 2007 (Vol. 27, No. 12)

Ribosomal Database Project II

  • Useful tools
  • Deep in geek
Before I was even aware that there was a Ribosomal Database Project I—Bam—the Ribosomal Database Project II had arrived. This database is aimed at providing online analysis, rRNA-derived phylogenetic trees, and various aligned and annotated rRNA sequences. Sounds like the site might have been better named the Ribosomal RNA Database Project instead. The tools at the Ribosomal Database Project II look to be quite useful for researchers. They include myRDP (align and classify 16S rRNA sequences), Tree Builder (create phylogenetic trees), Hierarchy Browser (for browsing phylogenetic hierarchies and compiling lists of 16S rRNAs), Classifier (assign 16S rRNA sequences to the taxonomical hierarchy), Sequence Match (upload sequences and search for nearest neighbors), Probe Match (match probes to database sequences). Yes, this is a site pretty much for RNA geeks only. The collection of tools is most welcome, however.
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