How to download and install OligoArray?



 
 
 
 
 

       OligoArray is distributed under the GNU GPL license (here is the License text in html or plain text). This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. I distribute freely the code to the community so please feel free to modify it and distribute your modifications under the terms of the GNU GPL license. If you modify it or find some bug, I will be happy to be kept in touch. I will also appreciate any feedback concerning any possible modifications to improve this software. If you definitively feel sad to do not pay for that software, you are welcome to support the Free Software Foundation.

        OligoArray is written in JavaTM. I am new in the programming field, so my code is far to be perfect. Any remarks are welcome ! One of my beginner's mistake was to write the code in one single long file. If you want to have a look to the code, it is right here (HTML code was generated from Java code using java2html). If you want to modify OligoArray, you just need to download the license gpl.txt and the code: OligoArray.java

        OligoArray was successfully tested on Windows 98 Second Edition, Windows NT4, Linux Red Hat 7.1 and Solaris 2.7. It should run on every systems where both Java and Blast run. Some users experienced unexpected behavior under MAC OS X (cross-hybridization never detected if you use Apple/Genentech BLAST) or under Red Hat 7.3 (No access to Mfold server). I strongly encourage all users to run extensive tests using test files given on this web site before to start a real design.
 

Before to start installation
        You need to create a folder where to install OligoArray and all other files. The path to this directory SHOULD NOT contain any funny characters like a space, ' or ".  In other terms, windows users, please avoid something like C:\Program Files\OligoArray.
C:\oligoarray will work properly. I will use this path for all examples presented below.

        Since OligoArray is written in Java, you need to verify that a Java Runtime Environment version 1.3 or more is installed on your computer. For Unix users, just type the command java -version. For Windows users, you will need to open a MS-DOS Prompt windows (it should be present in the Start menu). If Java is not installed or too old, you can get a JRE version 1.4 from SUN.
 
 

Download OligoArray and Blast
        I have created a package containing OligoArray, the license and a test file. Please download this package into the oligoarray folder you have just created. If you just want OligoArray.jar, it's here. I strongly encourage you to send me an email if you download OligoArray. It is the only way for me to announce you future versions of OligoArray or bug corrections. You will also need to download Blast in the same directory

UNIX

OligoArray.tar.gz (2.8 MB).
Blast (From NCBI, choose the right version for your OS).
Windows
OligoArray.zip (2.8 MB).
Blast for Windows from NCBI.
Install OligoArray
UNIX
To extract files, type   tar -xvzf OligoArray.tar.gz
The UNIX package contains 3 files (License.txt, OligoArray.jar and yeast_orf.fas)
Windows
To extract all files, use a tool like winzip. Make sure that you extract all files into the oligoarray folder.
The windows package contains 4 files (License.txt, OligoArray.bat, OligoArray.jar and yeast_orf.fas)
Install Blast
 
        Blast comes with complete installation instruction. Here are UNIX or Windows sections. Instead of using the NCBI's E.coli sequence file. If you do not know how to configure a PATH on Windows, just install Blast in the same folder as OligoArray.
Format a Local Blast Database
        Before to use OligoArray, you have to create a Blast database. This database should contain all sequences against which you want to the oligo specificity. For oligo designed for gene expression experiments, this database should contain only transcribed sequence for the organism you are working on. The blast database name SHOULD NOT contains any characters like a space, ' or ".

        The first step is to create a Fasta file containing all these sequences. Fasta format is one comment line preceded by a >  (look at the yeast_orf.fas file for an example of Fasta format). The sequence will appear on the next lines. I strongly suggest to use simple comment lines containing only one unique identifier. These identifier should be used also for the input file.

UNIX

To format a blast database from the yeast_orf.fas file, type :
        formatdb -i yeast_orf.fas -p F -o T
Windows
First, open an MS-DOS Prompt windows.
Go to the OligoArray folder. If the path to this directory is c:\oligoarray, just type at the prompt:
        cd c:\oligoarray
If you want to see the files present in this directory, type
        dir
If you have installed Blast and the fasta file you would like to format (yeast_orf.fas in this example), type:
        formatdb -i yeast_orf.fas -p F -o T

To test if Blast is working properly, type:
        blastall -p blastn -d yeast_orf.fas -i yeast_orf.fas
If many blast output appear in the windows, Blast is working properly. You can stop it using Ctrl C

Here is what your prompt windows should look like just before to start Blast: