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RNASTAR, Greengenes , and QIIMEdb

RNASTAR, Greengenes , and QIIMEdb. Rob Knight HHMI/CU Boulder. What: collection of RNA alignments backed by crystal or NMR structures (148 alignments, 9600 unique seqs ), cleaned up for isostericity (83% -> 94 isosteric bp )

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RNASTAR, Greengenes , and QIIMEdb

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  1. RNASTAR, Greengenes, and QIIMEdb Rob Knight HHMI/CU Boulder

  2. What: collection of RNA alignments backed by crystal or NMR structures (148 alignments, 9600 unique seqs), cleaned up for isostericity (83% -> 94 isostericbp) • Why: Provide training set for secondary structure and motif prediction, include both natural and artificial RNA • How: Align with BoulderALE • Who: My lab + Paul Gardner + ROC Alignment Ontology group; Eric Nawrocki; Craig Zirbel; NASA/HHMI/ROC ($) • Where: Alignments available from RNA web site with article, doi:10.1261/rna.032052.111 . AddingtoRfam.

  3. What: 408,315 (>1 million for Aug 1 release) near-full-length SSU rRNA sequences with tree and taxonomy • Why: Match environmental seqs to known SSU rRNA • How: Download seqs from INSDC; align to good seed model with infernal; transfer names from previous taxonomy; manual cleanup • Who: Authors; Adam Arkin, Sean Eddy; DOE/Sloan/HHMI/Gates ($) • Where: http://greengenes.lbl.gov/

  4. What: >4 billion 16S rRNA fragments from well-characterized environments • Why: Understand distribution of organisms in environment through meta-analyses across studies • How: Use QIIME (Quantitative Insights Into Microbial Ecology) to process next-gen amplicon data with consistent protocol; annotate with MIxS standard for metadata • Who: Jesse Stombaugh, Doug Wendel, Gail Ackermann; Jeff Gordon; Greg Caporaso; GSC; EMP Steering Committee; DOE/NIH/Sloan/HHMI/Gates ($) • Where: http://www.microbio.me/qiime

  5. The Future • Move from 16S/shotgun to complete genomes (this is happening now, theoretically 1000/HiSeq run) • Will be able to link all RNAs, not just 16S, to environment they come from • Challenges: find RNAs given very large numbers of incomplete but homologous genomes, align them efficiently, relate to environmental parameters

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