A quick primer for gene identification can be found on the front page of Tetrahymena Genome Database (http://ciliate.org/index.php/home/welcome), along with information on a convenient optional
way to store your bioinformatic searches for gene naming assignments and make them available to the community (Supra DB).
Thanks again for your help in annotating gene and published papers in TGD.
Jeff Kapler
On 12/3/12 5:25 PM, "Kapler, Geoffrey M." <[log in to unmask]">[log in to unmask]>
wrote:
December
3, 2012
Dear Ciliate Molecular Biology Researcher,
Here is your chance to make a meaningful contribution to the greater Ciliate Molecular Biology
community. The Tetrahymena Genome Database (TGD) is a Wiki-based community run database, curated by Nick Stover. A larger percentage of the genes in TGD are currently designated as hypothetical proteins, yet a simple BLAST analysis provides a strong indication
of what these proteins do. TGD simply does nothave the resources to do manual annotation of the genome and literature.
On behalf of the Tetrahymena Research Advisory
Board (TETRA), I am requesting that you participate in a community-wide effort to manually annotate TGD. This will serve several important purposes. (1) It will facilitate the extraction of gene information from the database for you and your colleagues, (2)
it will link published papers to genes in TGD, something we sorely need, but do not have the financial resources to support, and (3) it will help secure funds to maintain and further develop TGD, which is modestly funded by an NIH Tetrahymena Stock Center
grant. The renewal of the stock center grant will be submitted in the Spring of 2013. Consequently, we are asking that you make your personal contribution to updating TGD during the next three months. The number of Wiki edits, as well as the number of
originating sources of those edits are recorded. The final tally at Stock Center grant renewal time will provide reviewers with an indication as to whether this unique, community-driven approach to database curation is worth investing in.
We ask that you set a manageable goal in the next two weeks, and transmit that information
to Nick Stover to avoid unwanted duplicative efforts. The main objectives are to edit TGD by (i) naming genes and (ii) annotating
your own literature (and hopefully that ofothers working in your area of interest). For example, using BLAST, an undergraduate in my lab identified ~150 Tetrahymena genes in DNA replication and repair pathways that were previously catalogued as ‘hypothetical
protein’. She will assign gene names to TGD using the simple Wiki editing functions. Paramecium researchers should get involved and annotate TGD as well, based on information they have from their own research. If the work is spread around between labs and
within labs, a lot can be accomplished.
Nick has written a concise guide for BLAST-based bioinformatic identification of Tetrahymena
genes that is posted on the TGDsite and is attached to this email as a PDF file. He has also set up second website to deposit data files, so there is a record of who did the work and what the sequence alignments and e values look like. Our collective effort
to populate TGD with this low hanging fruit canmake a big difference. Please give as generously of your time as you can.
Jeff Kapler
TETRA Board: Doug Chalker, Ted Clark, Bob Coyne, Pam Geyer, Jeff Kapler, Kazufumi Mochizuki,
Carolyn Price, Nick Stover (ex officio)