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The standard design wizard for creating SureSelect DNA designs finds probes by tiling across the specified target regions at the indicated density. You define the target regions by entering identifiers for the genes of interest (with or without UTR regions, introns, and flanking bases) or by inputting specific genomic coordinates. Any orphan probes — i.e., probes with no adjacent or overlapping probes — are duplicated to improve their capture performance.
The advanced SureSelect DNA wizard offers multiple tiling-based approaches for adding probes to the design. The Tile Genes or Regions option uses the same method as the standard wizard. The Select Optimized Probes option, which is offered for human genome designs, is similar to the Tile Genes or Regions option in that it allows you to specify the regions of interest by entering target genes or genomic coordinates. But it differs in that it, instead of tiling across the target regions at a particular density, it uses a machine learning algorithm to select high-quality probes that cover the desired targets. Probes are selected based on multiple metrics of quality including specificity, GC content, and entropy. Probe density varies between 1x and 5x depending on target properties such as the uniqueness of the target sequence in the genome, GC content, and target size. Notably, the Select Optimized Probes option excludes orphan probes from the probegroup.
In the standard SureSelect RNA design wizard, you define the target RNA regions by entering your transcripts or genes of interest. When the inputted target is an identifier for a gene, SureDesign locates all of the RNA transcripts for that gene that are present in the selected transcriptome. It then uses those transcript sequences to perform transcript tiling, in which the SureDesign algorithm finds probes by tiling across the transcript sequences at the indicated density.
Like the standard SureSelect RNA wizard, the advanced SureSelect RNA wizard also offers the transcript tiling approach for adding probes to the design. Additionally, the advanced wizard offers a genomic tiling option. This option allows you to define the target regions by entering either gene identifiers or genomic coordinates. The SureDesign algorithm then finds probes by tiling across the selected DNA sequences at the indicated density, much as it does when finding probes for a standard SureSelect DNA design.
When using the genomic tiling approach for a SureSelect RNA design, the DNA sequence is used as a consensus target sequence for the various transcripts for the gene of interest. Thus, SureSelect RNA designs created with this method can be used both for both DNA and RNA captures. By contrast, the transcript tiling approach will tile across each transcript individually, ensuring a higher coverage for each transcript.
See Also
Create a SureSelect DNA design
Create a SureSelect RNA design
Guidelines on creating advanced designs