SYNOPSIS
	pscan -q multifastafile -p multifastafile [options]
	pscan -p multifastafile [options]
	pscan -q multifastafile -M matrixfile [options]

OPTIONS
	[-q file] | Specify the multifasta file containing the foreground sequences.

	[-p file] | Specify the multifasta file containing the background sequences.

	[-m file] | Use it if the background data are already available in a file (see -g option).

	[-M file] | Scan the foreground sequences using only the Jaspar/Transfac matrix file contained in the specified file.

	[-l file] | Use the matrices contained in that file (for matrix file format see below).

	[-N name] | Use only the matrix with that name (usable only in association with -l).

	[-ss] | Perform single strand only analysis.

	[-rs] | Perform single strand only analysis on the reverse strand.

	[-split num1 num2] | Sequences are scanned only from position num1 and for num2 nucleotides.

	[-trashn] | Discards sequences containing "N".

	[-n] | Oligos containing "N" will not be discarded. Instead a "N" will obtain an "average" score.

	[-g] | If a background sequences file is used than a file will be written containing the data calculated 
	       for that background sequences and the current set of matrices. 
	       From now on one can use that file (-m option) instead of the sequences file for faster processing.

	[-ui file] | An index of the background file will be used to avoid duplicated sequences. 

	[-bi] | Build an index of the background sequences file (to be used later with the -ui option). 
		This is useful when you have duplicated sequences in your background that may introduce a bias in your results.

	[-h] | Display this help.
	
NOTES
	The sequences to be used with Pscan have to be promoter sequences. 
        To obtain meaningful results it's critical that the background and the foreground sequences are consistent between them either in size 
        and in position (with respect to the transcription start site). For optimal results the foreground set should be a subset of the background set. 

	If the "-l" option is not used Pscan will try to find Jaspar/Transfac matrix files in the current folder. 
        Jaspar files have ".pfm" extension while Transfac ones have ".pro" extension. 
        If Jaspar matrix files are used than a file called "matrix_list.txt" must be present in the same folder. 
        That file contains required info about the matrices in the ".pfm" files.
	
	For info on how Pscan works pleare refer to the paper.

EXAMPLES

1)	pscan -p human_450_50.fasta -bi
	
	This command will scan the file "human_450_50.fasta" using the matrices in the current folder. 
	It is handy to use that command the first time one uses a set of matrices with a given background sequences file. 
	A file called human_450_50.short_matrix will be written and it can be used from now on every time you want to use 
	the same background sequences with the same set of matrices.  A file called human_450_50.index will be written too 
	and it will be useful every time you will use the same background file.
	
2)	pscan -q human_nfy_targets.fasta -m human_450_50.short_matrix -ui human_450_50.index
	
	This command will scan the file human_nfy_targets.fasta searching for over-represented binding sites (with respect 
	to the preprocessed background contained in the "human_450_50.short_matrix" file) using the matrices in the current folder. 
	Please note that the query file "human_nfy_targets.fasta" must be a subset of the sequences contained in the background file "human_450_50.fasta" 
	in order to use the index file with the "-ui" option. This means that both the sequences and their FASTA headers used in the query file must appear
	in the background file as well. Using the "-ui" option when the sequences contained in the query file are not a subset of the background file will
	have undefined/unpredictable outcomes.	
	The output will be a file called "human_nfy_targets.fasta.res" where you will find all the used matrices sorted by ascending P-value. 
	The lower the P-value obtained by a matrix, the higher are the chances that the transcription factor associated to that matrix 
	is a regulator of the input promoter sequences. 
	The fields of the output are the following: "Transcription Factor Name", "Matrix ID", "Z Score", "Pvalue", "Foreground Average", "Background Average".    
	
3)	pscan -q human_nfy_targets.fasta -M MA0108.pfm
	
	This command will scan the sequences file "human_nfy_targets.fasta" using the matrix contained in "MA0108.pfm". 
	The result will be written in a file called "human_nfy_targets.fasta.ris" where you will find the sequences in input 
	sorted by a descending score (between 1 and 0). The higher the score, the better is the oligo found with respect to the used matrix.
	The fields of the output are the following: "Sequence Header", "Score", "Position from the end of sequence", "Oligo that obtained the score", 
	"Strand where the oligo was found".

4)	pscan -p human_450_50.fasta -bi -l matrixfile.wil

	This command is like Example #1 with the difference that the matrices set to be used is the one contained in the "matrixfile.wil" file. 
	Please look at the "example_matrix_file.wil" file included in this Pscan distribution to see the correct format for matrices file.
	
5)	pscan -q human_nfy_targets.fasta -l matrixfile.wil -N MATRIX1

	This command is like Example #3 but it will use the matrix called "MATRIX1" contained in the "matrixfile.wil" file.
