R-COFFEE HOME PAGE

Multiple RNA Sequence Alignments

• What Is R-Coffee?

R-Coffee is a multiple sequence alignment package specificaly designed for RNA. Given a set of RNA sequences, R-Coffee generates a multiple sequence alignment using structural information. R-Coffee is included in the main distribution of T-Coffee (Version 5.60 or higher).

• How Does It Work

R-Coffee uses RNAlpfold to compute the secondary structure of the provided sequences. A modified version of T-Coffee is then used to compute the multiple sequence alignment having the best agreement with the sequences and the structures. R-Coffee can be combined with any existing sequence alignment method

• Related Publications

• R-Coffee: A Method for Multiple Alignment of Non-Coding RNA Andreas Wilm, Desmond G. Higgins & C�dric Notredame.N.A.R. (in press)

• Downloading T-Coffee and related packages

• Please download the latest T-Coffee version and its documentation T-Coffee Home page
• Previous versions are available on request: cedric.notredame@gmail.com
• To make the best of R-Coffee you will also need to install the following packages:
  
  
  • RNAlpfold frorm the vienna package (Compulsory) [*]
  • Mafft [*]
  • Muscle [*]
  • ProbCons [*]
  • ConSan [*]

• Using R-Coffee: Documentation and Tutorials

• Simplest usage:

  • t_coffee -mode rcoffee sequence_file
    Requires RNAlpfold to be installed
  • t_coffee -mode rcoffee_fast_approximate sequence_file
    Requires Mafft, Muscle, ProbConsRNA and RNAlpfold
  • t_coffee -mode rcoffee_slow_accurate sequence_file
    Requires Consan and RNAlpfold to be installed



• Download the documentation from

  • README
  • Tutorial: [doc] [html] [Examples Data]
  • Technical Notes: [doc] [html] [Examples Data]

• Servers

R-Coffee is currently only available on the main server, but drop me a line if you want to set up a mirror.

Available R_coffee servers:

• [server.tcoffee.org]