This repository documents recipes to discover cis-regulatory motifs within proximal promoters of plants in RSAT::Plants.
The reports and data in folder peach/ correspond to the benchmark experiment with peach expression-based gene modules. You can browse them at eead-csic-compbio.github.io/coexpression_motif_discovery/peach .
Citation: N Ksouri(1), JA Castro-Mondragón (2,3), F Montardit-Tardà (1), J van Helden (2), B Contreras-Moreira (1,4,5), Y Gogorcena (1) (2021) Tuning promoter boundaries improves regulatory motif discovery in non-model plants: the peach example. Plant Physiology, https://doi.org/10.1093/plphys/kiaa091
Questions or comments, please contact: nksouri at eead.csic.es
A docker container with Regulatory Sequence Analysis Tools (RSAT) image is available here. If you have not set a docker engine on your machine, please see the instructions provided by the docker community for a simplified installation procedure.
Once docker is set up, you can get and run the RSAT docker image by typing the following command lines in the terminal:
# Get the docker image docker pull ksouri1/rsat_nksouri # Run the docker container docker run --rm -v ~/rsat_data:/packages/rsat/public_html/data/ -v ~/rsat_results:/home/rsat_user/rsat_results -it ksouri1/rsat_nksouri
“rsat_results” and “rsat_data” are two local directories in the host machine serving as a persistant storage volume inside the RSAT docker container.
This work was partly funded by the Spanish Ministry of Economy and Competitiveness grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the Government of Aragón with grants A44 and A09_17R, which were co-financed with FEDER funds. N Ksouri was hired by project AGL2014-52063R and now funded by a PhD fellowship awarded by the Government of Aragón and co-financed with ESF funds respectively.