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Welcome to the home of the Tetrahymena Genome Database
(TGD).
TGD is a web-accessible database of information about the Tetrahymena thermophila genome sequence
determined at The Institute for Genomic Research (TIGR). TGD provides information on the genome, genes,
and proteins of Tetrahymena collected from the scientific literature,
research community, and many other sources.
TGD is intended to be a resource for all members of the scientific research
community interested in Tetrahymena and other ciliates. As
we develop TGD, we would greatly appreciate input from the
community so that we can better tailor TGD to meet its needs.
Please feel free to send comments, suggestions, or questions to TGD at
ciliate-curator@genome.stanford.edu.
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What's new at TGD |
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Eukaryotic Genome Annotation and Analysis Course
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TIGR is offering an external course called "Eukaryotic Annotation and
Analysis" that will present TIGR's eukaryotic annotation
methods and resources, as well as available open-source tools that
attendees can use externally. The course is being offered at TIGR
March 6-8, June 26-28, and September 18-20, 2007.
(February 27, 2007)
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FASEB Ciliate Molecular Biology Conference
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The next FASEB Ciliate MB Conference will take place July 21-26, 2007 in Tucson,
Arizona. Information on this meeting can be found at the FASEB Summer
Research Conferences web site (http://src.faseb.org/).
(November 29, 2006)
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Tetrahymena Genome Paper
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Eisen
and collaborators have published
a paper on the Tetrahymena MAC genome in
the September 2006 issue of PLoS Biology
(August 31, 2006)
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Model Organism BLAST Hits
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The table in the Homologs section of each gene's Locus page now displays the top BLAST
hits (based on E-values) resulting from a BLASTP comparison of the
predicted Tetrahymena proteins against various model organism databases. The
organisms we performed our comparisons with are:
Saccharomyces cerevisiae (SGD)
Drosophila melanogaster (FlyBase)
Caenorhabditis elegans (WormBase)
Homo sapiens (IPI (HUMAN))
Dictyostelium discoideum (dictyBase)
Paramecium tetraurelia (ParameciumDB)
Plasmodium falciparum (PlasmoDB)
Toxoplasma gondii (ToxoDB)
Cryptosporidium parvum (CryptoDB)
If no BLAST hit below 1.0e-02 was found for the gene in that organism, no results are shown for that
organism.
(June 1, 2006)
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Stock Center
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The Tetrahymena
Stock Center at Cornell University is now open! The Stock Center is
currently accepting orders for a core group of commonly requested
strains. Browse the list of strains available, then email or FAX your
order to the Stock Center. The Stock Center is also accepting
deposition of scientifically useful strains.
(March 23, 2006)
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Literature Guide
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We are now displaying the Literature Guide, which is designed to help
you sift through the Tetrahymena literature for a given gene
and find specific information. TGD performs weekly searches of the
PubMed literature to capture all of the papers mentioning each gene,
its aliases, and the keyword "Tetrahymena". TGD curators read
these papers and assign them to one or more Literature Topics that
describe the kind of biological information they contain on a given gene.
You can access a gene's Literature Guide from the "Additional
References and Literature Guide" link on its Locus page. As an
example, you can view the PDD1
Literature
Guide.
(January 18, 2006)
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GBrowse Annotation Update
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We have made updates to the data presented in our genome browser. Now, each of the
~300 protein-coding genes described in the Tetrahymena literature are
annotated with the standardized gene name, plus text from the brief descriptions we have curated for each gene. These gene models
now also appear in orange, making them easy to spot as you scan along a chromosome.
(January 17, 2006)
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2006 NAR Database Paper on TGD
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The 2006 Nucleic Acids Research Database
issue is now available. This issue includes a paper (HTML | PDF) by the TGD staff describing the resources for Tetrahymena research.
(January 1, 2006)
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TGD Expands Full-text Literature Search
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The TGD full-text literature search capability (powered by Textpresso) has been expanded to include 1100 Tetrahymena-related full-text journal articles. The full-text literature search can be accessed directly via the Textpresso link on the Home page and as a link from the Tetrahymena Literature page. For more information please see Textpresso Help.
(December 15, 2005)
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Gene Summary Paragraphs and References
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We have begun to write paragraph-long summaries of genes that are being displayed on the Locus Page. These summaries contain published biological information for a gene and its product, and are designed to familiarize both ciliate and non-ciliate researchers with important facts about a gene. They are written using natural language and a controlled vocabulary based on the Gene Ontology (GO), and contain references and hyperlinks to further information; they also highlight connections between genes from ciliate and other species wherever possible.
We are also now displaying references on the Locus Page for the Gene Name, Alias, Name Description, Description, and Summary Paragraph. When references are available, a citation number is displayed after the referenced information and is hyperlinked to its full citation listed at the bottom of the curated portion of the Locus Page. Beneath each reference is a hyperlink to the TGD curated paper or its PubMed citation, both of which display the reference's abstract when available.
For an example of a Gene Summary Paragraph and References, please see the Locus Page for PDD1.
(October 5, 2005)
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Quick Search Modifications
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We have made several changes to Quick Search. Now, when you use Quick Search to query TGD and your query matches keywords in more than one category, you will be redirected to the summary TGD Quick Search Results page, which lists the number of matches to each of the categories. This will enable you to view all of the information in TGD that may be relevant to your query. If your query only matches one gene name and nothing else in any of the other categories, then you will be redirected to the gene page.
We also added the category Paper Abstracts to those that are already queried by Quick Search: Gene Names, Gene Descriptions, GO Terms, Domains, Homologs, Colleagues, and Authors. To facilitate finding predicted protein domains, we separated out the category Domains from Gene Descriptions in the Quick Search Results page. For more information please see Quick Search Help.
(August 17, 2005)
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TGD's Tetrahymena Gene Index
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We have added an index of Tetrahymena thermophila genes that have been given standard gene names by the research community. The database and gene index page will be updated as new genes are discovered and published. Hyperlinks to the gene index may be found from the table of content categories Genome Resources and Tetrahymena Literature, located on the upper left hand side of the page.
(August 17, 2005)
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News Archive
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