OligoArrayDb, the Source of Microarray Probes for
Synechococcus sp. JA-2-3B'a(2-13)
Probe set created on 2006-11-16.
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[Source of Commercial Oligonucleotide Microarrays for Synechococcus sp. JA-2-3B'a(2-13)]


The Synechococcus sp. JA-2-3B'a(2-13) genome is provided in 1 piece of sequence ( CP000240 ) representing a total of 2862 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 58%, with a minimum and a maximum of 36% and 69% respectively. Ninety percent of these sequences have a GC content comprised between 50%and 63%. These values have been used to set OligoArray options during design. Here is the parameter set used for this particular design.

This database contains 7852 oligonucleotides to represent the Synechococcus sp. JA-2-3B'a(2-13) transcriptome. Among these 7852 oligonucleotides, 7254 are considered to be fully specific to their targets according to the design parameters described above.  In other terms, this database provides oligonucleotides for 2824 transcripts and 2695 (94% 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 Synechococcus sp. JA-2-3B'a(2-13).
 

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