Finding an ORF:
As described in the previous pages, you can find an ORF or ORFs in a number of ways. You can
search by: PlasmoDB ID or description, Automated Prediction ID or Annotation, GO Annotation or Number,
common gene name, functional group, or chromosome. Once your ORF of interest has been identified
by one of these searches, you will be sent to an ORF page.
ORF page
The ORF page (shown below) contains two sections: the ORF map and ORF table.
ORF map
The ORF 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.
ORF table
The ORF table, on the righthand side of the page, includes the ORF's PlasmoDB ID and description, as
well as a common gene name, if there is one. Clicking on the PlasmoDB ID will link you to the corresponding
page on the PlasmoDB website. Oligonucleotide IDC data is displayed below the
PlasmoDB ID and description, for the oligonucleotides that map to this ORF. Clicking on the 'OligoID' will take you
to the appropriate Oligo page. The oligonucleotide information displayed is: OligoID, its uniqueness in the genome,
the times of relative maximum and minimum expression, amplitude of expression, FFT score, phase, and CGH data (% of 3D7
intensity).
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