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

Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website ().

[1]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

[2]  Michael P. S. Brown,et al.  Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars , 2000, ISMB.

[3]  Hideo Matsuda,et al.  fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood , 1994, Comput. Appl. Biosci..

[4]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.

[5]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[6]  James R. Cole,et al.  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis , 2004, Nucleic Acids Res..

[7]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[8]  J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[9]  Sudhir Kumar,et al.  MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment , 2004, Briefings Bioinform..

[10]  Stephen L. Rathbun,et al.  Quantitative Comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples , 2001, Applied and Environmental Microbiology.

[11]  A. J. Jones,et al.  At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies , 2005, Applied and Environmental Microbiology.

[12]  Antonia J. Jones,et al.  At least one in twenty 16 S rRNA sequence records currently held in public 1 repositories estimated to contain substantial anomalies , 2005 .

[13]  References , 1971 .

[14]  Andrew P. Martin Phylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities , 2002, Applied and Environmental Microbiology.

[15]  Thomas L. Madden,et al.  BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..

[16]  J. Handelsman,et al.  Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness , 2005, Applied and Environmental Microbiology.

[17]  A. Halpern,et al.  Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. , 2000, Molecular biology and evolution.

[18]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.