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This is an OLD SITE
(5/2006)

  GO TO THE UPDATED SITE with all three strains: HB3, 3D7, and Dd2 and all the same search functions.
Step-by-step guide to this website:
Finding an Oligonucleotide:

As previously described, you can find an oligonucleotide or multiple oligonucleotides using the various query options. Once a specific oligonucleotide of interest has been identified, you will be sent to the appropriate oligonucleotide page.
Oligonucleotide page
The oligonucleotide page (shown below) contains five sections: oligonucleotide IDC data, oligonucleotide map, expression data, expression map, and oligonucleotide table.
Oligonucleotide IDC data
oligo data
This top table displays all IDC data associated with the oligonucleotide of interest: OligoID, uniqueness, hour of maximum and minimum relative expression, amplitude of expression, FFT score, phase, and CGH data.

Oligonucleotide map
The Oligo map on the left side of the page displays the position of the ORF of interest. On top, the entire chromosome where this ORF maps to is displayed. The location of the ORF, plus the surrounding 100 kb is highlighted on the chromosome in red. In the second box, the ORF plus the surrounding 100 kb is displayed. The 10 kb surrounding the ORF is highlighed in a red box. The third box displays this 10 kb, centered around the ORF of interest. All unique oligonucleotides in this 10 kb region are displayed as black triangles. Finally, the bottom box displays the entire ORF. All unique oligonucleotides that map to the ORF are displayed as black triangles. Additionally, you can move along the chromosome to surrounding ORFs using the right and left arrows below this map.









Oligonucleotide expression graph
In the middle of the page, the expression data for the oligonucleotide of interest is displayed as a graph of log ratio(cy5/cy3) versus time. As you scroll your mouse arrow over the graph, it changes from non-scaled to scaled. A black point represents a good data point. A white spot represents a bad data point. A red spot represents the average of multiple data for that point in the IDC.












Oligonucleotide expression map
The Oligonucleotide expression map on the right side of the page displays the oligonucleotide's expression data as the log ratio(cy5/cy3) from -2 to 2. The surrounding 20 oligonucleotides' expression data is also displayed.

















Oligonucleotide-ORF data
ORF data This bottom table displays PlasmoDB ORF information, oligonucleotide sequence, and Automated prediction information associated with the oligonucleotide. Clicking on the PlasmoDB ID will send you back to the ORF page on this website. You can also BLAST the oligonucleotide sequence by clicking on the link: 'BLAST @ PlasmoDB'. Finally, clicking on any of the Automated predictions will link you to the appropriate page on PlasmoDB.org.
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