About TGD Wiki

      Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University funded by a grant from the National Institutes of Health (A RESOURCE CENTER FOR TETRAHYMENA THERMOPHILA, awarded to Theodore Clark at Cornell University). Our mission is to collect and display annotations of the Tetrahymena thermophila genome, sequenced at The Institute of Genomic Research by Jonathan A. Eisen, et al. from 2003-2006. The Tetrahymena genome paper was published in PLoS Genetics in 2006. Work on the TGD project was published in the Nucleic Acids Research Database Issue (Stover, N.A, et. al, 2006).

As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD:

  • Gene Names and Aliases
  • Gene Descriptions
  • Gene Ontology (GO) Annotations
  • Homologs (similar genes in selected organisms)
  • Protein Domains
  • Associated Literature
  • Paragraphs (longer, free-text descriptions of gene function, structure, and significance)
  • Coding and Protein Sequences

      However, during the four-year suspension of curation at TGD, many sequence updates were released by TIGR and about 500 new journal articles were published on Tetrahymena genes. Much of the information was based on the original gene models released by TIGR from 2004-2006. Changes to the Tetrahymena gene models, as well as updates in other databases, have undoubtedly rendered some of the original descriptions, homologs, and domains inaccurate. We are planning to update these fields to better reflect the current gene model sequences. At the moment we have updated the following fields to match the newest gene model sequences (TIGR v.2008):

  • Coding and Protein Sequences
  • Protein Domains
  • Gene Descriptions

      We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface.

      A final note on the organization of TGD Wiki. The TGD Wiki database is housed at Bradley University, but two other tools, the TGD GBrowse Genome Browser and the TGD BLAST server, are currently maintained at Stanford University. Gene sequences in the GBrowse, BLAST, and Wiki databases are maintained separately, and at the present time only the sequences in the Wiki have been updated to TIGR v.2008. We will be working to update the gene model sequences used by these tools in the future when time permits. For now, please be aware of the sequence variations among these different parts of the website. Users will be notified when updates to these sequences are made.

Please feel free to send comments, suggestions, or questions about TGD Wiki at ciliate-curator@bradley.edu

TGD Wiki Staff

Current Staff - Bradley University:


Nick Stover, PhD
Principal Investigator
Assistant Professor
Department of Biology

Ravinder Punia
Lead Programmer
Graduate Student
Department of Computer Science and Information Systems

Mike Bowen
Programmer and GUI Developer
Graduate Student
Department of Computer Science and Information Systems

Additional contributions made by:


Steven Dolins, PhD
Assoc. Prof. and Department Chair
Department of Computer Science and Information Systems

Alex Uskov, PhD
Assistant Professor
Department of Computer Science and Information Systems

Anudeep Singh, MS
Research Assistant
Department of Computer Science and Information Systems