The Xylella fastidiosa 9a5c genome is provided in 3 pieces of sequence ( AE003849, AE003850, AE003851 ) representing a total of 2832 transcripts. These sequences have been analized for their GC content as this is an important parameter for probe design. The average GC content of these coding sequences is 52%, with a minimum and a maximum of 19% and 72% respectively. Ninety percent of these sequences have a GC content comprised between 40%and 62%. These values have been used to set OligoArray options during design. Here is the parameter set used for this particular design.
This database contains 7338 oligonucleotides to represent the Xylella fastidiosa 9a5c
transcriptome. Among these 7338 oligonucleotides, 6345 are considered
to be fully specific to their targets according to the design parameters described
above. In other terms, this database provides oligonucleotides for
2789 transcripts and 2482 (87% of all sequences)
have at least one specific oligo representing them. The figure below gives details on the number of CDS with specific probes.
Understanding this graph:
In the best case, you want the proportion of black and red genes to be as small as possible. Black ones are the genes with no probe at all. These genes will always be missing on your array. Red ones are the sequences for which OligoArray was not able to find a specific probes. However, it reported a non-specific probe. Our thresholds to define specific probes are quite conservative and many non-specific probes will actually prove to be specific in a real experiment. All other genes (blue, yellow and green) have at least one specific probe. While the number of genes with 3 specific probes may vary greatly from an organism to another, this may have little effect on your microarray design. Indeed, many will prefer to have one probe per gene, this probe being replicated several times on the array rather than having several probes per gene with less replicates.
Here we report the transcripts that do not have any oligonucleotide at all or any specific oligonucleotides.
With all these data in mind, you may want to access to the oligonucleotide
page where you can download a microarray probe set representing the coding sequences of Xylella fastidiosa 9a5c.
[OligoArrayDb Home Page]