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Profs Package for relate Domain with Proteins Families

Uses the definitions given by CATH domains for expands the information obtained through profiles of Pfam database.

Features

The pipeline has capacity to relate the structural information of CATH with sequence information of Pfam, construction of libraries by families or clans. If the information is not available CATH, a alignment process is developed. In Addition, fragmented, repeat domains and domains formed by several families (supradomain) are supported. Please refer to the main wiki Profs for more background information.

Requirements

Instructions

  1. Clone the Profs repository: $ git clone https://bitbucket.org/afgiraldofo/profs.git.
  2. Build the Profs R package: $ R CMD build profs.
  3. Install Profs R package: $ sudo R CMD INSTALL ./Profs_0.99.tar.gz --no-lock --clean. If package installed successfully, go to the next step.
  4. Load the Profs package from inside the R terminal by typing > require("Profs"). To find the location of external binaries type: > system.file("bin",package = "Profs").
  5. Add the location of external binaries to the system path variable. This can be done by adding the export PATH="path:$PATH"; line to the "~/.bashrc" file, where path is the path to external binaries found in step 4.

NOTE: The R version was testing with the 3.10 version, 2.14.1 or lower have compatibility problems.