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TGD News Archive
TTLL Genes Added to TGD
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We have added fifty tubulin tyrosine ligase-like genes (TTLL's) to our database. Members of this gene family were shown in a recent article in the journal Science to be responsible for tubulin polyglutamylation signals that direct intracellular transport. Congratualtions to the authors of the article, including members of the Gaertig Lab, on this important finding. To see the list of TTLL genes in Tetrahymena, enter "TTLL*" into the Quick Search box at TGD.
(June 28, 2005)
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Preliminary Gene Name Synchronization
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As part of the data synchronization effort between TIGR and TGD, we have updated the names used to identify the preliminary gene models at our site to match those shown at TIGR. The "PreTt" names used to identify these gene models at TGD are still stored here and are shown in the "Alias" field for each preliminary gene. These names can still be used to search for your genes of interest.
(June 9, 2005)
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TGD Help Pages
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We now have help pages available online that will hopefully answer many of your questions. We will be continuing to add information to these help pages as well as introduce new ones. If you still have questions please feel free to contact us at ciliate-curator@genome.stanford.edu. A hyperlink to Help is available in the table of contents on the left hand side of the page or in the toolbar on the top of locus pages.
(May 26, 2005)
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TGD Tutorial
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We are now presenting an online Tutorial to help familiarize everyone
with
some of the pages and tools that can be found at our site. In this tutorial
we
walk through basic features of the Locus Page, the GBrowse genome
browser
utility, full-text literature searches using Textpresso, and more. Enjoy!
(May 12, 2005)
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Gene Annotations; Genome Browser
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TGD created automatic annotations for TIGR's ~27,000 preliminary T. thermophila gene models based on a variety of sequence analysis tools. Using the Quick Search tool you can now query these annotations for your favorite genes (for example enter "beta-catenin" and look under Homologs), proteins containing conserved domains (enter "chromo", then look in Descriptions), proteins localized to specific regions of the cell (enter "mitochondrial membrane", then explore Gene Ontology terms), and more.
TGD curators have used the literature to prepare short, searchable descriptions for the ~200 macronuclear genes previously deposited in public databases. These descriptions, along with links to references associated with these genes, are shown with information about the corresponding preliminary gene model, if available (e.g. PDD1, GRL4).
The preliminary protein and predicted RNA genes of TIGR's chromosomal genome sequence can now be scanned using GBrowse, a popular tool provided as part of the Generic Model Organism Database project (GMOD). Click on the Genome Browser window from a gene page to view that gene's local genomic region, or go directly to TGD GBrowse to search the genome for gene names, protein descriptions, genomic coordinates, or even short nucleotide sequences.
We hope you enjoy exploring all the new information on our enhanced site. More features are under development, but we do need your feedback about what is useful for your research, and what new features would help you locate the information you need. Please email us at ciliate-curator@genome.stanford.edu with any suggestions or comments you have.
(May 2, 2005)
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TIGR Deposits Genome Sequence in Genbank
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The most recent assembly (Assembly 2) of the T. thermophila macronuclear genome sequence
has been deposited in Genbank's Whole Genome Shotgun (WGS) section by Jonathan Eisen and his team at TIGR. Congratulations to everyone working on the sequencing project on this milestone!
The genome sequence can now be searched at TGD using BLAST. In addition to BLAST, we offer the option to search this (and our other sequence datasets) with BLAT, an extremely fast search tool designed to locate long stretches of identity. This tool is ideal for identifying genomic versions of EST or other cDNA sequences, and for locating previously sequenced genome features.
(March 1, 2005)
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BLAST Search
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BLAST
searching of T. thermophila sequences is now available through
TGD. DNA and protein datasets for T. thermophila, and for Class
Oligohymenophorea, were assembled from international sequence databases (GenBank,
EMBL, DDBJ, RefSeq, SwissProt, PIR, PRF, and PDB) and can be searched using WU BLAST 2.0. The T. thermophila genome
sequence generated by TIGR will be available for BLAST at TGD soon.
(February 7, 2005)
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Preview GO Annotations
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Gene Ontology (GO)
annotations are now shown on the ten preview gene pages (e.g. PDD1). Many of
these genes feature new terms, definition changes, or modifications to
the ontology structure proposed by TGD to accommodate the unique
aspects of ciliate biology. It is now possible to search for Tetrahymena
genes annotated to a particular GO term by entering the term into the
Quick Search. For an example, see the results of this search for "elimination".
TGD also offers a graphical view of the ontology on
each GO term page (e.g "DNA
Binding"). Explore nearby regions of the GO using this handy interface.
(February 17, 2005)
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TGD Features Preview
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A number of new features are now available from TGD:
Tetrahymena
Labs provides a list of Tetrahymena labs, with
associated keywords and links to publications for each lab.
(January 21, 2005)
TGD Textpresso
offers full-text searching of 800 Tetrahymena research articles, plus
many more abstracts and titles.
Colleague
Search allows you to add or retrieve your personal colleague
page at TGD, or view the pages of other
Tetrahymena researchers.
Preview sample Locus pages for the following genes: ACTIN,
PDD1,
TWI1, TERT, GRL1, TIF1, ERF1, BTU1, HHT1, DYH1
(January 20, 2005)
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Site Upgrades
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TGD is undergoing a website redesign to more easily interface
with our new database. If you would like to see information posted on, or
linked from this site, please email the TGD curators at ciliate-curator@genome.stanford.edu.
Thank you for your suggestions.
(December 7, 2004)
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TIGR Releases Preliminary Gene Predictions
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TIGR releases preliminary gene
predictions for the Tetrahymena thermophila genome, which is
available for BLAST
search and for FTP download via their website.
(September 9, 2004)
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Tetrahymena Genome Sequencing Press Release
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Press
release from the National Institute of General Medical Sciences, NIH
about the Tetrahymena Genome
Sequencing Project led by
scientists at TIGR.
(April 9, 2003)
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To contact TGD: Send email to ciliate-curator@genome.stanford.edu.
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