OligoArrayDb, the Source of Microarray Probes for
Treponema pallidum subsp. pallidum str. Nichols
Probe set created on 2009-11-13, updated on 2009-11-13.
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[Source of Commercial Oligonucleotide Microarrays for Treponema pallidum subsp. pallidum str. Nichols]


The Treponema pallidum subsp. pallidum str. Nichols genome is provided in 1 piece of sequence ( AE000520 ) representing a total of 1031 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 37% and 69% respectively. Ninety percent of these sequences have a GC content comprised between 45%and 59%. These values have been used to set OligoArray options during design. Here is the parameter set used for this particular design.

This database contains 2898 oligonucleotides to represent the Treponema pallidum subsp. pallidum str. Nichols transcriptome. Among these 2898 oligonucleotides, 2844 are considered to be fully specific to their targets according to the design parameters described above.  In other terms, this database provides oligonucleotides for 1020 transcripts and 1009 (97% 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 Treponema pallidum subsp. pallidum str. Nichols.
 

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