raDI

raDI (reduced alphabet Direct Information) is a variation of the direct-coupling analysis (DCA) algorithm that groups physico-chemically equivalent amino acids prior to the computation of DCA. raDI achieves similar results than the original DCA while reducing the computation time by more than 30-fold for sequences with length of ~1,000 residues. Moreover, raDI overcomes the quality of predictions based on mutual information (MI); the accuracies and distributions of contacts predicted by raDI are higher and more useful than those predicted using MI, while reducing the time of computation more than 180-fold.

Please cite: ...

Content

The repository is organized as follows:

• The bin folder contains the raDI executable
• The msa folder contains scripts for multiple sequence alignment construction
• The src folder contains the raDI code

Dependencies

RADI requires the following dependencies: ...

Installation

raDI is written in C programming language.

To compile the code, type make from within the src folder. This will create a raDI executable file both in the src and ./bin/ folders.

Usage

Execution of raDI depends on the user being allowed to use an unlimited number of processors, a feature normally blocked in unix-based systems.

This property can be re-written for bash:

ulimit -s unlimited

or for csh:

limit stacksize unlimited

or for MacOS:

ulimit -s 65532

Without this, the executable will rise a segmentation fault. As this parameters do not affect normal functionality of the system, we recommend to add the command to the ~/.bashrc or ~/.cshrc configuration file.

Call raDI -h to see the options of the executable:

./raDI -h

#          Program for Mutual Information and Direct Information between positions of a Multiple Sequence Alignment(MSA)
#          It includes the possibility to check contact-pairs using a PDB file
#          Authors:
#                 Bernat Anton, Mireia Besalú, Gemma de las Cuevas,
#                 Oriol Fornes, Jaume Bonet, Narcis Fernandez-Fuentes
#                 Baldo Oliva
#          Structural Bioinformatics lab (GRIB)
#          Universitat Pompeu Fabra
#          Catalonia
#          Contact: baldo.oliva@upf.edu  (+34 933160509)
#          Last Update: March 2018


	 -msa 		 File with Multiple Sequence Alignments (MSA)
	 -ssa 		 File with Secondary Structure (SS) aligned with the seed in the MSA file
	 -xsa 		 File with sequence of PDB structure aligned with the seed in the MSA file
	 -pdb 		 PDB File of the SINGLE chain structure of the seed
	 -sdis		 Minimum distance in sequence between residue-pairs (default 10)
	 -lfrg		 Fragment length to avoid redundant results (selecting the best pair between two fragments, default 5)
	 -ra  		 Reduced alphabet of AA (default is no-reduction:0)
	      		    0 {-}{A}{C}{D}{E}{F}{G}{H}{I}{K}{L}{M}{N}{P}{Q}{R}{S}{T}{V}{W}{Y}
	      		    1 {-}{RKH}{DE}{STNQ}{AVLIM}{FWY}{C}{G}{P}
	      		    2 {-}{RKHDESTNQC}{AVLIMFWY}{G}{P}
	      		    3 {-}{RKHDESTNQCG}{AVLIMFWYP}
	 -o   		 Root name of the outputs with MI, DI and Contact-Map data for GNU plot.
	 -swap		 Swap the AA (or raAA) without affecting gaps
	 -v   		 Verbose
	 -h   		 This help (if MSA file is null help is also shown)