RepeatExplorer2 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.
How to user RepeatExplorer2:
- RepeatExplorer2 can be used through Galaxy based web interface on our public server at address https://galaxy-elixir.cerit-sc.cz. This server is provided as part of the Elixir CZ project and is maintained by CESNET and CERIT-SC that are participants of this project.
- Source code for local installation of RepeatExplorer2 can be found here. Basic documentation can be found in wiki.
- Step by step protocols were published in Nature Protocols (free link to the full text). Protocols include detailed instruction how to perform:
- De novo repeat identification in a single species
- Comparative repeat analysis in a set of species
- Development of satellite DNA probes for cytogenetic experiments
- Identification of centromeric repeats based on ChIP-seq data
Source code for the old version of RepeatExplorer server can be downloaded from Bitbucket.
Example of output from RepeatExplorer2:
You need to create user account on galaxy server to access example data The following datasets and processing were generated according above referenced protocols.
- De novo repeat identification in a single species
- Comparative repeat analysis in a set of species
- Using TAREAN for development of satellite DNA probes for cytogenetic experiments
- Identification of centromeric repeats based on ChIP-seq data
SeqGrapher
SeqGrapheR is a program for vizualization in exploration of sequence based graphs generated in RepeatExplorer output. SeqGrapheR program is now deposited in github repository. See also our SeqGrapheR manual and input data examples.
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
Examples of RepeatExplorer can be found in:
Macas, J., Novak, P., Pellicer, J., Cizkova, J., Koblizkova, A., Neumann, P., Fukova, I., Dolezel, J., Kelly, L., Leitch, I. (2015) – In depth characterization of repetitive DNA in 23 plant genomes reveals sources of genome size variation in the legume tribe Fabeae. PLoS ONE 10: e0143424.
Dodsworth, S., Chase, M.W., Kelly, L.J., Leitch, I.J., Macas, J., Novak, P., Piednoël, M., Weiss-Schneeweiss, H., Leitch, A. (2015) – Genomic repeat abundances contain phylogenetic signal. Syst. Biol. 64: 112-126.
Novak, P., Hribova, E., Neumann, P., Koblizkova, A., Dolezel, J., Macas, J. (2014) – Genome-wide analysis of repeat diversity across the family Musaceae. PLoS ONE 9: e98918.