Oligowiz Commands

Open terminal. Go to Oligowiz directory. Run the following commands:

perl ow2.format.pl -g PpaTranscriptome-2009-08-13.fasta -dbname db_Ppa_20090813 -speciesname Ppa_20090813

perl oligowiz2.pl -in PpaTranscriptome-2009-08-13.fasta -species db_Ppa_20090813 -length 60 -lmax 60 -lmin 60 -minlh 15 -posscoretype 3 > Ppa_20090813.owz
- ProbeLength = 60, Minimum Homology threshold for cross-hybridization = 15, Probes bias = towards 3' end.
java -Xmx300m -jar OligoWiz-2.1.3.jar
- This will bring up the GUI. Load the .owz file. Specify the following score weights:
  - Cross-Hyb = 5
  - Delta-Tm = 5
  - Folding = 1
  - Position = 5
  - Low-complexity = 0.7
- Click place oligos. Specify following parameters:
  - Min distance between oligos = 90bp
  - Max. number of oligos//sequence = 5
  - Minimum total score allowed = 0.7
  - Click "Apply to All" button.
- Export oligos and the missing probes list to a tab file and a fasta file respectively.
- Format the OligoWiz probes using perl scripts into a "complete/tdt" format compatible with eArray.
- Upload the probes to eArray [1]. Use them in a microarray design.

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