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*                                                                             *
*                                  GENPORTRAIT                                *
*                                  version 1.0                                *
*                                Purdue University                            *
*                             Bin Li and Daisuke Kihara                       *
*                                                                             *
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AUTHORS:
GenPortrait are developed by Bin Li <lib@purdue.edu> and Professor Daisuke Kihara <dkihara@purdue.edu> Group in Purdue University.

Department of Biological Sciences/Computer Sciences
Purdue University
Lilly Hall, 915 West State St.
West Lafayette, IN 47907-2054
tel: 765-496-2284; fax:765-496-1189

genPortrait can display the portrait of the genome by counting the frequencies of n-mer (n<=9) WORD in genome sequences (fasta format) and mapping to color bitmap pictures. It is written in C++, and it can be compiled and used in both Windows and UNIX.

INSTALL: 
It use the CImg Library, which can be download from http://cimg.sourceforge.net/index.shtml, CImg.h is included in the package, the current version is 1.08.
Two applications are developed in this package:
1. fasta2asc:
fasta2asc will read the genome sequences and count the frequences of 9-mer WORD, then save the counts in asc file format to avoid read the long genome sequence repeatly.
2. genPortrait:
genPortrait will read the asc format file and map the frequencies to gray scale by normalizing to 0-255 or map to color by using HSV, JET, COOL, and SPRING method.
To compile the project, copy the source code to any directory, and run make to compile. if you meet any problem, please send email to lib@purdue.edu.

USAGE: 
fasta2asc <fasta files> will generate a asc file named as <fasta files>.asc, for example: fasta2asc ecoli.fna will generate the ecoli.fna.asc file.

genPortrait will display or generate the portrait by using: 
./genPortrait [options] target
       -s save to bmp file
       -d show bmp file in windows
       -m using mean method instead of log method
       -B Black/White output
       -H HSV output
       -J JET output
       -C COOL output
       -S SPRING output
       -n n=1..9, width
Sample:
./genPortrait -sHJCS ecoli.fna.asc will generate four bitmap files: ecoli.fna.asc.HSV.bmp, ecoli.fna.asc.JET.bmp, ecoli.fna.asc.COOL.bmp, and ecoli.fna.asc.SPRING.bmp

LICENSE: the GNU Public License

19/03/2005