Please go to OligoPicker Homepage for more detailed descriptions and the latest version (http://pga.mgh.harvard.edu/oligopicker/index.html).

Files in this directory.

1) OligoPicker2.3.1.pl. This is the main program file for probe design.

2) NCBI_format.pl. This script is to add pseudo GI numbers to the beginning of all FASTA definition lines. You should not run this script if your sequence file is already in NCBI FASTA format. However, you have to run this script before using OligoPicker if your FASTA file is not in NCBI format (i.e. definition line does not start with 'gi|...'). In this case, please use the output file from this script as input sequence file for OligoPicker. This file only modifies the definition lines without making any change to your sequences.


3) test.fasta. This is a sample sequence file containing 25 sequences in NCBI FASTA format. You should be able to generate unique probes using this sample file if you have successfully set up OligoPicker in your Linux computer.

4) rna.fasta. This file contains non-messenger RNAs from human, mouse, and rat. You might want to use it as a filter file for your oligo design (for more details, go to OligoPicker Homepage).

5) gpl_license.txt. This is a GPL license file attached to this program.

6) NCBI directory. This directory contains two plug-in programs (BLAST and DUST) from NCBI. Please do not make any changes in this directory.