PROFdisis

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Contents

Intro

profdisis (DISIS) - Accurate prediction of the residues that bind DNA directly from amino acid sequence without requiring any additional experimental or structural information.

Availability/Web server

This program can be run through the PredictProtein service.

Installation with aptitude (Debian, Ubuntu, etc.)

Software Installation

  1. If you have not done so until now, add the rostlab repository to the list of your syanptic package manager. This is how it's done: Debian_repository#sources.list.d
  2. aptitude update
  3. aptitude (search for rostlab keyring and install by marking the package with a '+' and hit 'g' twice to install)
  4. aptitude update (to determine all rostlab packages to install)
  5. aptitude install profdisis. Here's a step by step guide Debian_repository#Installing_a_package_step_by_step

Generating Input Files for profdisis

profdisis can take an alignment profile file as an input:

  • filtered_hssp_file - PSI-BLAST alignment profile file.

Generating an HSSP Input File

Here is a protocol for converting an alignment to an HSSP profile.

Running PROFdisis

Please see the PROFdisis man page:

 man profdisis

Reference

Prediction of DNA-binding residues from sequence, Yanay Ofran, Venkatesh Mysore and Burkhard Rost. Bioinformatics, Vol. 23 ISMB/ECCB 2007, pages i347–i353

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