Sequence Quality

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Sequence Quality

• Up to 1/3 of sequences from a clone library are
  putative chimeras.
• Comprehensive chimera screening of public data
  using newly-developed Bellerophon3.
• Provides quality-controlled set for probe
  selection.

Sequence Count
Sequence Source
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Taxonomy in Flux
Each yellow dot represents a named phyla

• Incongruent taxonomic nomenclature even at phylum
  level.
• Making multiple taxonomic classifications
  available through Greengenes will aid in
  standardizing classification, particularly for
  environmental lineages.
• Greengenes integrates each, allowing a balanced
  approach to nomenclature of newly discovered
  organisms.
• EXAMPLE Halanaerobium salsugo
• HugenholtzBacteria Haloanaerobiales
  Haloanaerobiaceae Haloanaerobium/ Haloincola
• LudwigBacteria Haloanaerobiales
  Haloanaerobiacae Haloanaerobium
• PaceBacteria Haloanaerobiales
  Haloanaerobiaceae Haloanaerobium/ Haloincola
• RDPBacteria Firmicutes Clostridia
  Halanaerobiales Halanaerobiaceae Halanaerobium
• NCBIBacteria Firmicutes Clostridia
  Halanaerobiales Halanaerobiaceae Halanaerobium

Only a fraction of the phyla are recognized by
all five major curators.
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Probe/Primer Design

• Check phylogenetic scope of a primer or probe.

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Web-accessible repository for DNA microarray data.

• Password protected Database is being developed to
  allow authorized users to search for bacteria of
  interest by city or by time (date). Weather data
  corresponding to the collection dates will be
  linked.
• Given that there are over 9,000 OTUs detectable
  per chip, the database will provide information
  on more than 2 million data points that can be
  viewed in relation to weather patterns.

Example of how bacterial groups can be mapped to
geographic location.
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D1D2 analysis

• 12,422 aligned D1D1 regions are in our database
• representing 1909 fungal taxa (according to
  annotation distributed by NCBI
• 5,488 OTUs were found.
• 2,283 OTUs had 1 or more great probes
• 3,801 OTUs had a distributed solution
• 4,828 OTUs have probes that could all be
  triggered by lt 5 other OTUs