Ciliate.org
Genome databases for the ciliate research community
Posted on 2024-10-09 14:45:24 by ciliate-curator
The reannotated T. thermophila gene models generated by the Gao Lab at OUC are ready for release at TGD. We will be making updates to the site, including the genome browser and BLAST server, to prepare for the update beginning Thursday 10/10. TGD may become unavailable during this time; our other genome databases and SUPRDB should be unaffected. Thank you for your patience while we upgrade the TGD site.
Posted on 2024-08-09 11:06:32 by ciliate-curator
TetraMANIA is a tool developed at the University of Toronto, based on the popular GeneMANIA platform, that helps you predict the function of your favorite Tetrahymena genes and gene sets. GeneMANIA finds other genes that are related to one or more input genes using co-expression, protein domain similarity, physical interaction, and other data. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen, or find new genes with a specific function.
See the network for each gene on its TGD page, or begin a new search at TetraMANIA. Special thanks to Ron Pearlman and the GeneMANIA team for bringing this tool to the ciliate research community!Posted on 2024-07-22 22:07:23 by ciliate-curator
The full version of Tetrahymena Gene Network Explorer (TGNE) is now available at TGD. Visit Resources > TGNE Genome Files on this page to access and read the TGNE Quick Start Guide. To use the TGNE dashboard, download the HTML files and open them locally in a web browser. Thanks to Lev Tsypin, Michael Bertagna, and Aaron Turkewitz for developing this tool for the ciliate research community!
Posted on 2024-07-19 12:48:39 by ciliate-curator
The Genome Browser and BLAST server at BlepharismaDB have begun showing slightly skewed results compared to the actual gene and protein sequences. We are not aware of this problem at other Ciliate.org databases. We appreciate your patience while we work to resolve this issue at BlepharismaDB.
Posted on 2023-09-18 12:54:11 by ciliate-curator
We have revamped the arrangement of files under the Genome Data tab found under the Resources menu on TGD. The last annotation of the Tetrahymena thermophila genome was published in 2020, and was the fifth version of genome files to be released to the community. We have labeled these "v5" in the file handles, to help denote them as the latest genome files, and to distinguish them from previous and future versions. The other three Tetrahymena species hosted at TGD (elliotti, borealis, and malaccensis) were only sequenced and annotated once to date, and are labeled "v1". All other files available at the site are listed by date under "Legacy Files". If you have any questions, please contact us at ciliate-curator@bradley.edu
Posted on 2023-09-18 12:54:11 by ciliate-curator
We have revamped the arrangement of files under the Genome Data tab found under the Resources menu on TGD. The last annotation of the Tetrahymena thermophila genome was published in 2020, and was the fifth version of genome files to be released to the community. We have labeled these "v5" in the file handles, to help denote them as the latest genome files, and to distinguish them from previous and future versions. The other three Tetrahymena species hosted at TGD (elliotti, borealis, and malaccensis) were only sequenced and annotated once to date, and are labeled "v1". All other files available at the site are listed by date under "Legacy Files". If you have any questions, please contact us at ciliate-curator@bradley.edu
Posted on 2023-04-03 21:43:54 by ciliate-curator
The 2023 Ciliate Molecular Biology Meeting will be held from June 26 to 29, 2023 in Montpellier, France. The early registration and abstract submission deadline is April 15, with late registration extending until May 15.
For questions related to the registration and requesting a letter for your visa application, please send an e-mail to ciliatemeeting@123events.fr. For more details, please visit the meeting website at: https://www.ciliate-meeting-2023.com/en/Posted on 2023-04-03 21:43:54 by ciliate-curator
The 2023 Ciliate Molecular Biology Meeting will be held from June 26 to 29, 2023 in Montpellier, France. The early registration and abstract submission deadline is April 15, with late registration extending until May 15.
For questions related to the registration and requesting a letter for your visa application, please send an e-mail to ciliatemeeting@123events.fr. For more details, please visit the meeting website at: https://www.ciliate-meeting-2023.com/en/Posted on 2022-11-17 14:45:17 by ciliate-curator
Tetrahymena Genome Database Wiki is currently undergoing scheduled website updates. We have replaced the GBrowse genome browser with JBrowse2 and are using this GMOD software to display the T. thermophila macronuclear and micronuclear genome sequences. We have also created a new BLAST server interface. Several community database edits from the last year will be added back before December 1. The T. malaccensis, T. elliotti, and T. borealis genomes will be displayed in JBrowse2 in the next month.
Posted on 2022-11-17 14:45:17 by ciliate-curator
Tetrahymena Genome Database Wiki is currently undergoing scheduled website updates. We have replaced the GBrowse genome browser with JBrowse2 and are using this GMOD software to display the T. thermophila macronuclear and micronuclear genome sequences. We have also created a new BLAST server interface. Several community database edits from the last year will be added back before December 1. The T. malaccensis, T. elliotti, and T. borealis genomes will be displayed in JBrowse2 in the next month.
Posted on 2021-10-29 00:24:36 by ciliate-curator
We have made changes to OxyDB to reflect the latest reannotation of the genome. Gene names displayed on OxyDB pages have been changed and now link to the updated genome browser. The previous annotation can still be searched using the BLAST server and legacy GBrowse genome browser.
Posted on 2021-03-22 00:00:00 by ciliate-curator
This Special Issue is open to reporting all studies on ciliates as model organisms, seeking to understand their genetics, cell biology, biochemistry, evolution, ecological adaptation, and the complex mechanisms of signaling systems, from the genes involved to the changes in gene expression during cell response, and from the structure and involved evolution of signal molecules to the membrane traffic in the cells. The deadline for submission is 31 December 2021. We look forward to receiving your contributions. Prof. Dr. Cristina Miceli Prof. Dr. Adriana Vallesi Guest Editors Dr. Ronald Edward Pearlman Co-Guest Editor
Posted on 2021-03-22 00:00:00 by ciliate-curator
A new paper on methods to identify protein interactions in Tetrahymena has been published. Functional proteomics protocol for the identification of interaction partners in Tetrahymena thermophila. Congratulations to the authors!
Posted on 2021-03-22 00:00:00 by ciliate-curator
This Special Issue is open to reporting all studies on ciliates as model organisms, seeking to understand their genetics, cell biology, biochemistry, evolution, ecological adaptation, and the complex mechanisms of signaling systems, from the genes involved to the changes in gene expression during cell response, and from the structure and involved evolution of signal molecules to the membrane traffic in the cells. The deadline for submission is 31 December 2021. We look forward to receiving your contributions. Prof. Dr. Cristina Miceli Prof. Dr. Adriana Vallesi Guest Editors Dr. Ronald Edward Pearlman Co-Guest Editor
Posted on 2021-03-22 00:00:00 by ciliate-curator
A new paper on methods to identify protein interactions in Tetrahymena has been published. Functional proteomics protocol for the identification of interaction partners in Tetrahymena thermophila. Congratulations to the authors!
Posted on 2020-04-16 00:00:00 by ciliate-curator
We have received an update of the Tetrahymena thermophila genome sequence from researchers at Ocean University of China. The gene pages, BLAST server, and Genome Browser have all been updated accordingly to display these new data. Congratulations to the team involved in this effort!
A publication explaining the new sequences and features has been published:Posted on 2020-04-16 00:00:00 by ciliate-curator
We have received an update of the Tetrahymena thermophila genome sequence from researchers at Ocean University of China. The gene pages, BLAST server, and Genome Browser have all been updated accordingly to display these new data. Congratulations to the team involved in this effort!
A publication explaining the new sequences and features has been published:Posted on 2019-05-01 00:00:00 by ciliate-curator
A review of nuclear proteomics results described for Tetrahymena thermophila by Saettone, et al. has been published in the journal Genes. Congratulations to the authors!
Posted on 2019-05-01 00:00:00 by ciliate-curator
A review of nuclear proteomics results described for Tetrahymena thermophila by Saettone, et al. has been published in the journal Genes. Congratulations to the authors!
