Welcome to RepeatExplorer

Developed and maintained by the Laboratory of Molecular Cytogenetics , Institute of Plant Molecular Biology, Biology Centre AS CR, Ceske Budejovice, Czech Republic.


RepeatExplorer includes utilities for Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data and tools for the detection of transposable element protein coding domains. The server can be used without registration, but it is recommended to set up a free account allowing the use of advanced features like data and workflow sharing. Additionally, the available disk space is limited to 200Mb for unregistered users. Registered users are free to use up to 50Gb. Read RepeatExplorer documentation before analyzing data!

Server maintenance announcement

Our server at www.repeatexplorer.org was down for maintenance during March 3, 2017. All interrupted jobs must be restarted manually by user. We recommend to migrate your calculations to our new server at https://repeatexplorer-elixir.cerit-sc.cz..

6th Workshop on the Application of Next Generation
Sequencing to Repetitive DNA Analysis in Plants

May 23-25, 2017, Institute of Plant Molecular Biology, České Budějovice, Czech Republic

The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training.

The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). Registration is open till May 7, 2017. In case of any questions or comments please contact Jiri Macas.

 

How to Use RepeatExplorer

Major tools provided on the server

New RepeatExplorer server

We recommend to use alternative RepeatExplorer Galaxy server at address https://repeatexplorer-elixir.cerit-sc.cz. This server is should be preferred for processing larger datasets as it provides better computational and storage resources. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

How to Cite

If you use RepeatExplorer in your work please cite:

Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence reads. Bioinformatics


This work was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047) including access to computing and storage facilities. RepeatExplorer is a part of services provided by ELIXIR - European research infrastructure for biological information. For other services provided by ELIXIR's Czech Republic Node visit www.elixir-czech.cz/services .

ELIXIR

workload of server not available

References

The principles of RepeatExplorer approach are described in:

Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11: 378.

Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence reads. Bioinformatics

Repeat Explorer uses RepeatMasker and Repbase:

Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogentic and Genome Research 110:462-467

Clustering is performed using Louvain method:

Blondel V.D., Guillaume J., Lambiotte R., Lefebvre E. (2008) Fast unfolding of communities in large networks. J. Stat. Mech.: P10008

Terms of Use

RepeatExplorer is provided as free, public, Internet accessible service, in the hope that it will be useful, but WITHOUT ANY WARRANTY. Data transfer and data storage are not encrypted. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to setup your own local Galaxy instance with RepeatExplorer Alternatively, you can install only RepeatExplorer and use its command line version. If you need help with RepeatExplorer or you want to report a problem, please contact server administrator