OligoArrayDb, the Source of Microarray Probes for
Frankia sp. EAN1pec
Probe set created on 2008-07-07.
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[Source of Commercial Oligonucleotide Microarrays for Frankia sp. EAN1pec]


The Frankia sp. EAN1pec genome is provided in 1 piece of sequence ( CP000820 ) representing a total of 7191 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 70%, with a minimum and a maximum of 44% and 81% respectively. Ninety percent of these sequences have a GC content comprised between 63%and 76%. These values have been used to set OligoArray options during design. Here is the parameter set used for this particular design.

This database contains 20367 oligonucleotides to represent the Frankia sp. EAN1pec transcriptome. Among these 20367 oligonucleotides, 14368 are considered to be fully specific to their targets according to the design parameters described above.  In other terms, this database provides oligonucleotides for 7162 transcripts and 6163 (85% 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 Frankia sp. EAN1pec.
 

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