Ocimum OligoSets - Information
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The predesigned Ocimum Oligo Sets are identical with the oligo probes that we use for our validated OciChip series, therefore each Ocimum Oligo Set you buy is validated by our microarray development department and by our independent cooperation partners, leading experts in their respective research fields.
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Ocimum Oligo Sets are now available for all our catalog arrays. Each individual oligo has been designed using our proprietary design algorithms that ensure absolute gene specificity. Powerful bioinformatics delivers one probe per gene.
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Recent publications on the ideal length of oligonucleotide probes, as well as experimental evidence from our own research and development microarray department indicate that 50mer oligonucleotide probes represent an optimal balance of sensitivity and specificity for use in microarray technology.
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Extensive BLAST analysis against all coding regions of the organisms of interest.
Ocimum's approach to ensure high microarray quality is based on sophisticated bioinformatics tools like the Oligos4 Array software and our proprietary non-redundant CodeSeq databases. These software tools are part of our unique computational platform called Genowiz™ that allows the establishment of completely automated workflows e.g. for oligo probe design and microarray production.
Oligos4Array - several steps for designing the ideal oligo:
- Definition of oligo sequences based on physical parameters
- Length
- GC content
- Secondary structures
- Overlap between selected oligos
- Dimer formation
- Extensive alignments using the our non-redundant database CodeSeq to sort out unspecific sequences In order to select gene specific sequences, Oligos4Array compares the sequences designed with those of all known coding regions of the species of interest (BLAST and Smith-Watermann analysis). For that purpose a CodeSeq database containing all known coding regions of the respective species is generated (based on redundant public and proprietary databases). As it is quite common today that the identical sequence information is submitted several times to the same public database these databases are redundant information sources. However only databases that store each sequence once exclusively, that is non-redundant databases, can ensure automated, high throughput design. The reason is that for efficient comparisons between oligo sequences and sequences stored in databases, the parameter "each oligo sequence is allowd to occur once only" is clear without ambiguity. Therefore, we has established our proprietary CodeSeq database for each organism of interest.
- Application dependent selection of gene specific oligonucleotide probes (e.g.exon specific)
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High Purity Salt Free - HPSF® oligonucleotides Ocimum's software tool for oligo synthesis, Biotracker™, controls the fully automated production of the designed oligos in superior HPSF® quality. HPSF® oligonucleotides are the only that are
- 100% full length products (free of n-1 products and failure products)
- Free of salt and metal ions
- Standard QC and identity checked by MALDI-TOF analysis - oligonucleotide probes longer than 50mers cannot be checked by mass spectrometry
This constant high quality allows you standardized microarray production from batch to batch, and from chip to chip.
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Complete order process automation and high capacity guarantees error free, fast service
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Microplates, Aliquotation
Ocimum Oligo Sets are delivered in 96 or 384 well plates. If desired, probes and spotting buffer will be aliquoted to customer specifications.
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Ocimum's amino modified oligo probes are suitable for all slide surfaces
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OciChip™ array Concept
