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Microbial Genome Reannotation Workshop

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DOE Joint Genome Institute

Walnut Creek, California

The U.S. Department of Energy Joint Genome Institute (DOE JGI) is organizing a Microbial Genome Reannotation Workshop to be held at JGI in Walnut Creek, California, on January 19-20, 2012.

Attendance to this workshop is by invitation only

 

Participants

  • Victor Markowitz, DOE JGI
  • Nikos Kyrpides, DOE JGI
  • Natalia Ivanova, DOE JGI
  • Amrita Pati, DOE JGI
  • Denis Kaznadzey, DOE JGI
  • Jim Tripp, DOE JGI
  • Amy Chen, DOE JGI
  • Kostas Mavrommatis, DOE JGI
  • Tatiana Tatusova, Staff Scientist at National Center for Biotechnology Information (NCBI)
  • Granger Sutton, Senior Director of Informatics at the J. Craig Venter Institute (JCVI)
  • Jennifer Wortman, Director of Microbial Informatics at Broad Institute
  • Owen White, Director of Bioinformatics, Institute for Genome Sciences, University of Maryland
  • Mark Borodovsky, Director of Center for Bioinformatics and Computational Genomics, Georgia Tech University.

Agenda

Thursday, January 19
9:00-9:15 Welcome – Introductions
9:15-9:30 Workshop goals and approach
In each step below we will be discussing:

  1. Alternative methods used
  2. Proposed pipeline
  3. Implementation of confidence levels for feature prediction
  4. Benchmarking (when needed)
  5. QC and validation methods
Defining the reannotation pipeline
9:30-10.00 RNA calling methods and replication features
10:00-10:30 Repeat finding (eg CRISPR, IS elements) and Prophage finding
10:30-11:30 CDS finding
11:30-12:00 Transcription features finding (terminators, operons)
12:00-13:00 Lunch
13:00-14:00 Translational features (pseudogenes, stop codon recoding, RBS)
14:00-14:30 Feature precedence and overlap resolution
14:30-16:00 Benchmarking approach and method evaluation standards
16:00-17:00 Annotation metadata standards
Validation Methods:

  • RNA calling
    • All rRNAs and tRNAs must be present
    • rRNA sizes
  • CDS finding
    • Orthologs presence across strains of same species
    • Start site consistency
  • Repeat finding
  • Transcription features finding
  • Transcription features finding
  • Feature precedence and overlap resolution
    • No CDs should be overlapping rRNAs
Friday, January 20
9:00-12:00 Practical details of re-annotation pipeline

  1. Which genomes to re-annotate (finished genomes only? filter out model organisms?)
  2. Mapping between versions
  3. Who develops specific components or the entire pipeline
  4. Where the pipelineis implemented
  5. Where the re-annotation pipeline (or pipeline components) will run
  6. Where the data are stored and how are the provided to the community
  7. Future developments and maintenance of the pipeline
  8. Re-annotation refreshes process
12:00-13:00 Lunch
12:00-13:00 Annotation of new genomes
– Using this pipeline for the newly sequenced genomes
13:30-14:30 General discussion
– Funding
– Publication/white paper