To provide quality-controlled microbial DNA data and tools to researchers for rapid analysis of user-generated sequences. To construct 16S rRNA oligonucleotide probe arrays capable of detecting and quantifying prokaryotic organisms in complex environmental and clinical samples.

• Phase I (Sequence Database) Objectives:

  • Create comprehensive multiple sequence alignment which includes all full-length publicly available prokaryotic 16S rRNA sequences. Status: complete, periodically updated

  • Maintain complete prokaryotic taxonomic trees Status: complete, periodically updated

  • Cluster all high-quality sequences into Operational Taxonomic Units (OTUs) based solely on sequence similarities. Status: complete, periodically updated

  • Inform SSU rRNA scientists of annotation-sequence discrepancies in hopes of improving the public data repositories. Status: not initiated

  • Incorporate sequence quality assessment. Status: in progress

  • Apply an automated chimera check to filter or mark suspect sequences. Status: complete

  • Assimilate suggestions and hand curations from the greengenes user community to improve alignments, chimera assessments, and nomenclature. This will be done in a semi-automated fashion using the Curation Tools . Status: in progress

• Phase II (Sequence Workbench) Objectives:

  • Reduce the steps needed for basic 16S rRNA gene analysis in batch mode. The pipeline (chromatograms -- assembly -- alignment -- chimera evaluation -- classification -- distance matrix creation -- tree reconstruction -- sampling statistics) should be easy to enter at any point and allow collection of data from all downstream modules. Status: in progress

  • Establish user project folders for FTP upload/download of large data sets. Status: in progress

  • Allow greater customization of exported fields from greengenes records. Status: in progress

  • Implement batch BLAST and batch Simrank input/output. Status: in progress

• Phase III (Probe Array Design) Objectives:

  • Design effective probes which differentiate each OTU from all others. For each OTU identify approximately 25 probes that will hybridize to most members of the OTU and to no sequences (or only distantly related sequences) outside the OTU. Status: complete

  • Build a 500,000 feature Affymetrix microarray containing sets of probes for each OTU. Status: complete

• Phase IV (Probe Array Validation) Objectives:

  • Validate microarray design using synthetic defined microbial communities. Status: manuscript in review

• Phase V (Array Experiment Browser) Objectives:

  • Provide an interface with 16S rRNA microarray data generated from probes developed from the prokMSA sequence collection. Status: in progress