CisPlusFinder
predicts CRMs based on perfect local ungapped sequences through multiple
organisms

requirements
To run CisPlusFinder you need a global installation of blast on your computer
which is called by the command blastall. Additional you need the perl module
IxHash which is freely available on the internet


unpack
if you downloaded the program package CPF.tgz you can unpack it with the
command     
		tar -xzvf CPF.tgz

install
before you can run CisPlusFinder you have to compile it on your machine and
make the scripts executable. To compile CisPlusFinder and the additional C
programs, change to the directory bin with the command

		 cd CFP/bin
and type	 make
		 

To use a script which executes all steps of CisPlusFinder automatically go up
one directory to the directory CFP and type
	      
		chmod +x runCFP.pl

Maybe you also need to specify the directory, where CisPlusFinder is located
on your computer. This is done in the script runCPF.pl in line 10.

run
CisPlusFinder takes as input a multiple fasta file. To apply the program to a
multiple fasta file type

runCFP.pl <input file> [options]

if you want to change the options you can do it in the following way

OPTIONS FOR PLUS DEFINITION:

        -w              windowsize      (default: 1000)
        -c              length of the core      (default: 5)
        -ot             minimal overrepresentation of the core  (default: 2)

OPTIONS FOR CLUSTERING:

        -rp             minimal number of PLUSs in 500bp

OPTIONS FOR BED FILE:

-offset         genomic start position of the sequence in format chr?:start


output
The output of CisPlusFinder is written to the directory output. This directory
contains four to five files.

1. *.lst contains a list of the homologous positions of the pre alignment
    calculated with blast and mon2dis

2. *.cpf contains the maximal perfect local ungapped sequence starting at
    every position, its p-value and the relative positions of the hits in the
    other sequences

3. *.crm contains the local coordinates of the predicted CRMs

4. *.PLUS contains the significant PLUSs and their positions

5. *.bed is only produced when the option offset is chosen. This file contains
    can be uploaded at UCSC and shows the predictions in the genomic context 


test
We included some test files in the directory test, where you can try running
CisPlusFinder. To produce also the bed-file the command line is

./runCFP.pl test/hairy.fa -offset chr3L:8629705

and 

./runCFP.pl test/hairy.fa -offset chr2R:5471053

If you have any problems, questions or suggestions please e-mail:
  nora.pierstorff@uni-koeln.de