FedCloudRSAT

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General Information

  • Status: Preparatory
  • Start Date: 08/10/2014
  • End Date: -
  • EGI.eu contact: Nuno Ferreira / nuno.ferreira@egi.eu, Diego Scardaci / diego.scardaci@egi.eu
  • External contact: Jacques.van-Helden / Jacques.van-Helden@univ-amu.fr

Short Description

RSAT (Regulatory Sequence Analysis Tools) offers a series of tools dedicated to the detection of regulatory signals in non-coding sequences. The only input required is a list of genes of interest (e.g. a family of co-regulated genes). From this information, you can retrieve the upstream sequences over a desired distance, discover putative regulatory signals, search the matching positions for these signals in your original dataset or in whole genomes, and display the results graphically in the form of a feature map. Each tool is presented as a form to fill. For each form, a manual page provides detailed information about the parameters. RSAT usally processes data-sets extracted by the Ensembl databases

Use Case

A VM image embedding RSAT is already available. As a first test we would like to deploy one instance of this VM on the EGI Federated Cloud.

Requirements to run the RSAT VM:

  • 1 Core
  • 2 GB of RAM
  • 12 GB of storage

RSAT Data-sets can be huge, first tests will be done with a couple of genomes (about 4 GB). Later we will test RSAT with bigger data-sets.

Additional Files

RSAT web site: http://rsat.ulb.ac.be/