Stand alone version

First, this is the first version, so there will be many bugs that I will fix every day. I will do a complete tutorial in two weeks, to teach how to install and use it correctly. Also, I will develop a version for windows. Thanks in advance!

Requirements:

1. Mac OSX
2. Linux
3. The same RAM memory than your genome is (for human, 2.5 GB).
   
4. perl
5. Install Tk library:

perl -MCPAN -e shell
cpan> install Bundle::CPAN
cpan> reload cpan
cpan> install Tk


6. Install Bioperl:http://bioperl.open-bio.org/wiki/Installing_BioPerl

How to use it:

1. Download the zip file
2. Create a directory whatever you want
3. Unzip the file (dbl click)
4. Open a Terminal and go to the folder where is the file "proseek.pl"
   
5. type: perl proseek.pl
6. You will see the same parameters than in the web page
7. Fisrt you have to load the blat server. For that, you need to download all the chromosomes of the interested genome. From human click here. And save the fasta files in some folder that only contain the fasta files.
8. In the ProSeeK windows, click in Choose button. Select one chromosome of your genome.
9. Click in Load Blat button
10. Wait until in the terminal appears "Server ready for queries!"
    
11. Then, you can paste your sequence in the corresponding text and perform the analysis for any sequence. You have to wait until a new window showing the results appears to perform the next design.
12. Before closing ProSeeK please, click in Stop Blat button to release your memory RAM.