-
- 
-
-
- Developed and maintained by the Laboratory - of Molecular Cytogenetics, Institute of Plant Molecular Biology, - Biology Centre CAS, Ceske Budejovice, Czech Republic
-This RepeatExplorer Galaxy portal is a part of services provided - by ELIXIR - (European research infrastructure for biological information). Please - acknowledge this fact in your publications by adding a statement: - “Computational - resources for RepeatExplorer analysis were provided by the ELIXIR-CZ - project (LM2023055), part of the international ELIXIR - infrastructure.” -
- -
-
- Official Galaxy - Project website with information how to use the Galaxy platform -
-For command line version of the RepeatExplorer tools, see - the source code - repository -
-| - | - |
|---|---|
|
- Oct 23, 2020 - |
-
- Step by step protocols were published in - Nature Protocols- |
-
|
- Jan 13, 2020 - |
-
- Galaxy server was updated to version 19.09- |
-
|
- Jan 13, 2020 - |
-
- RepeatExplorer2 and TAREAN tools were updated - to version 2.3.7-See changelog for detailed description of included changes. - Previous versions can be found in Obsolete tools section - - |
-
|
- Jan 8, 2020 - |
-
- RepeatExplorer tools are now available in - Galaxy toolshed-Packages repeatexplorer2, dante and re_utils can be installed - from Galaxy toolshed to custom Galaxy instance if you prefer - analysis using RepeatExplorer on on your server. - |
-
|
- Nov 10, 2019 - |
-
- Data quota increased to 200G-Data quota for registered users was increased from 50G to 200G - to enable easier analysis of larger datasets - |
-
Information about changes in - RepeatExplorer programs can be found in its repository changelog. -
-If you need a help or you want to - report a problem, please contact server - administrator. -
-Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.
-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 29:792-793. -
-Classification of repetitive elements using REXdb:
-Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – - Systematic - survey of plant LTR-retrotransposons elucidates phylogenetic - relationships of their polyprotein domains and provides a reference - for element classification. Mobile DNA 10:1.
-The principle of repeat identification implemented in the - RepeatExplorer: -
-Novak, P., Neumann, P., Macas, J. (2010) - Graph-based - clustering and characterization of repetitive sequences in - next-generation sequencing data. BMC Bioinformatics - 11:378. -
-Using TAREAN for satellite repeat detection and - characterization: -
-Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, - P., Macas, J. (2017) - TAREAN: - a computational tool for identification and characterization of - satellite DNA from unassembled short reads. Nucleic Acid - Research 45:e111 -
-
-
- RepeatExplorer is provided as free, public, Internet accessible - service, in the hope that it will be useful, but WITHOUT ANY - WARRANTY. Data transfer are encrypted, but data storage are not. 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 -
-
-
-
-
Developed and maintained by the Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
+This RepeatExplorer Galaxy portal is a part of services provided by ELIXIR (European Research Infrastructure for Biological Information). Please acknowledge this fact in your publications by adding a statement: “Computational resources for RepeatExplorer analysis were provided by the ELIXIR-CZ project (LM2023055), part of the international ELIXIR infrastructure.”
+
If you need help, need to increase a data quota, or want to report a problem, please contact server administrator. If you encounter an error while running a tool, please report a bug using the bug icon in the dataset history.
+The RepeatExplorer server provides a suite of tools designed for the comprehensive analysis of repetitive DNA sequences in genomic data. Here are the most common use cases for utilizing these tools:
+Annotation of repeats directly from low coverage sequencing: It can be accomplished using the RepeatExplorer2 tool. This approach is ideal for initial exploration and annotation of repetitive sequences using low coverage data (refer to protocol 1 in the step-by-step protocols above).
Comparative analysis of repeats in multiple species from low coverage sequencing reads: Use protocol 2 for analyzing repetitive DNA across different species.
Tandem repeat annotation from low coverage sequencing: If your focus is primarily on tandem repeats, use the Tandem Repeat Analyzer tool (TAREAN). See protocol 3 in the step-by-step protocols for details.
Chip-Seq experiments: The ChIP-seq Mapper tool identifies centromeric repeats from CENH3 ChIP-seq data without the need for a complete genome assembly, leveraging assembled contigs from repeat clusters as a reference for mapping reads and highlighting significantly enriched repeats (refer to protocol 4).
Annotation of full-Length LTR-retrotransposons in genome assemblies: For detailed annotation of LTR-retrotransposons within assembled genomes, use the DANTE + DANTE_LTR tools. (see https://github.com/kavonrtep/dante_ltr for details)
Annotation of tandem repeats in genome assemblies: The TideCluster tools are designed for the annotation and analysis of tandem repeats within genome assemblies (see https://github.com/kavonrtep/TideCluster for more information).
Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.
+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 29:792-793.
+Classification of repetitive elements using REXdb:
+Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10:1.
+The principle of repeat identification implemented in the RepeatExplorer:
+Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378.
+Using TAREAN for satellite repeat detection and characterization:
+Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research 45:e111
+RepeatExplorer is provided as free, public, Internet accessible service, in the hope that it will be useful, but WITHOUT ANY WARRANTY. Data transfer are encrypted, but data storage is not. 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 set up 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.
+