Tuesday, August 28, 2007

Vinga Entropic Profiles

Instructions for using the software acconpanying BMC Bioinformatics manuscript:

The software to canculate Renyi entropic profiles is delivered as

1) Open source Matlab m-coded toolbox.

2) Stand alone executables for Windows, Mac and Linux. Each environmenty requires that a runtime server application (MCR) be downloaded and installed. For those who have Matlab installed, please note that most likely you will still need to install the appropriate MCR. The reason is that the stand alone executable files were produced for MCR 2006a so unless you have Matlab version 2006a you will need to also install the MCR listed below for your operating system. No Mathworks/Matlab licenses are needed.

2.1. WINDOWS: first install MCRinstaller 2006a for Windows and then unzip the files in renyi_bin_win.zip.

2.1. LINUX: first install MCRinstaller 2006a for Linux and then unzip the files in renyi_bin_lin.zip. (coming soon)

2.3 MACKINTOSH: first install MCRinstaller 2006a for Linux and then unzip the files in renyi_bin_mac.zip. (coming soon)

The execution of the executable code is similar to that of the m-code function vinga_entropic except that the input argumets are passed space delimited. For example, instead of using


one would use, at the commant line,

vinga_entropic m4.seq 6 12 253

The detailed help information for this function is provided below. Please note that the executable binary file will produce several export files. These include producing the figures in pdf and png formats and also exporting the numerical results of the calculations as an XML.

help on vinga_entropic:

VINGA_ENTROPIC is the main function of the toolbox for processing sequences
Syntax: vinga_entropic(fastafile,N,phi,position)
Description: this is the main function that calls all others and is the
right function to compile for sequence processing. The numerical results,
figures and intermediate calculations will be stored with names built
from the fasta file name. For example, if the fastafile is m4.seq, all
graphs and figures will be saved as m4_*.pdf and m4_*.png.
****Input arguments:
fastafile - text file with sequence to be analyised (in FASTA format)
N - kernel resolution parameter
phi - kernel smoothing parameter
position - local study of particular symbol in the original sequence
figure files with all the graphical results (see webpage)
XML page with numerical data

EXAMPLE: vinga_entropic('m4.seq',6,12,253)

NOTE: The compiled version takes char inputs, therefore the type conversion is
checked and corrected if needed
Authors: Susana Vinga and Jonas S Almeida
Reference: "Local Rényi entropic profiles of DNA sequences"
BMC Bioinformatics (submitted)
Version: 2007.08.27
Webpage: http://algos.inesc-id.pt/~svinga/ep/

Please write us at Susana Vinga <svinga@vinci.inesc-id.pt> if you need any assistance with teh installation or if you want to report any bugs.