Ocimum biosolutions offers microarays and bioinformatis sofftware to researchers across the world, The microaray division of ocimum offers the MWG chips which were earl;ier manufactured by MWG biotech of Germany
for more detail visit http://www.ocimumbio.com
OciChip™ Design – Route to a perfect Array
OciChip™ design and production concept ensure the highest microarray quality.
First, sophisticated bioinformatics design chips of the highest specificity and sensitivity – an advantage customers of other chip manufacturers do not have.
Second, the calculated oligonucleotides are produced and purified with strict quality control procedures including MALDI-TOF MS. Huge production capacities, know-how and process automation guarantee high quality and fast service at affordable prices. Moreover, our microarray experts and their cooperation partners do functional validation of each of the catalog arrays. Of course, every individual batch of arrays is quality controlled extensively.
The backbone of the array probe design are sophisticated bioinformatics tools such as the Oligos4Array software and our proprietary non-redundant CodeSeq databases. These software tools are part of our unique computational platform called BioGIST® that allows establishment of completely automated workflows; e.g., for oligo probe design and microarray production. Each individual oligo is designed using proprietary design algorithms that ensure absolute gene specificity with one probe per gene.
Oligos4Array – several steps for designing the ideal oligo for every single gene:
1. Design of an oligo probe begins with defining physical parameters such as
- GC Content
- Secondary structures
- Overlap between selected oligos
- Dimer formation
Extensive R&D efforts proved that 50mers meet the requirements for specificity and sensitivity the best. The default GC content setting is between 40 and 60%, but will be adjusted as required depending on the project. Obviously, the algorithms exclude oligos that show secondary structures, overlaps, and primer dimer formation. Thresholds can be defined individually.
2. Extensive alignments use our non-redundant database CodeSeq to sort out unspecific sequences
In order to find gene specific probes, Oligos4Array compares suggested 50mer sequences with those of all known coding regions of the species of interest (BLAST and Smith-Waterman 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 submission of identical sequence information several times to the same public database is quite common today, these databases are redundant information sources. However, only databases that store each sequence once exclusively, i.e., 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 allowed to occur once only” is clear without ambiguity. Therefore, we establish and update regularly our proprietary CodeSeq databases for each organism of interest.
First, all sequences available in public and proprietary databases for a specific organism are clustered, whereby each cluster represents one unique gene. Secondly, a consensus sequence or contig generated from each cluster is entered into our CodeSeq database and thus forms the basis for gene specific and automated oligo probe design.
3. Application dependent selection of gene specific oligonucleotide probes (e.g. exon specific, strain specific or alternative splicing)
4. Recent publications on the ideal length of oligonucleotide probes, as well as experimental evidence from our own research and development indicate that 40-50 mer oligonucleotide probes show an optimal balance of sensitivity and specificity.
5. Our laboratory information and management system Biotracker™ controls the fully automated production of the designed oligos in superior quality. Our oligonucleotides are
- Full length products purified from n-1 products and failure products
- Free of salt and metal ions
- Standard QC and identity checked by MALDI-TOF analysis
This constant high quality allows standardized microarray production from batch to batch, and from array to array
6. Complete order process automation and high capacity guarantee an error free and fast service.
Filed under: bioinformatics, Blogroll, microarray, outsource | 1 Comment »