Genorama™ Chip Design Software

PROGRAMS IN GENORAMA™ CHIP DESIGN SOFTWARE

1. PickSNP^TM – for SNP selection of large-scale genotyping.

The program is particularly optimised for selection of uniformly distributed set of SNPs over large chromosomal regions or over the whole genome. This is often required for determination of haplotype structure in certain regions of the chromosome.

User-defined number of SNPs can be selected from the human genome from certain chromosomes, certain chromosome regions, and around certain genes.

Users can specify additional information such as:

• Location relative to genes (exonic SNPs or genic SNPs)

• Maximum distance from the nearest exon (e.g. all SNPs within 3 kb from nearest exon)

• Minimum distance between two consecutive SNPs

• Haplotype block structure (select only haplotype tag SNPs)

2. ProbeDesigner^TM - for designing APEX primer

The program is for choosing APEX primers that are suitable for SNP genotyping by APEX. APEX primer testing is necessary to avoid false or failed signals due to secondary structure, dimer formation and direct repeats.

3. BioPrimer^TM - for PCR primer design

The program automatically select optimal PCR primers for large datasets of human SNPs. All PCR primers are tested against the human genome sequence to ensure that unique PCR product is amplified (see next paragraph for details).

Template sequence is automatically masked to avoid:

• Design of PCR primers over known SNPs

• Design of PCR primers in repeated regions

• Design of PCR primers that contain short direct repeats

4. GenomeTester^TM - for testing uniqueness of the primers

The program tests quickly user-provided PCR primers against the human genome. This is necessary to find and eliminate primers with excessive number of binding sites (to avoid failed PCR) and to find alternative PCR products (to avoid false signals in genotyping experiment). We have written extremely efficient programs GenomeMaskerTM and GenomeTesterTM for the Genome Test. Our Genome Test is optimised for the human genome, however other completely sequenced genomes can also be used.

5. MultiPLX^TM - grouping of PCR primers into groups according to their compatibility

The program calculates the optimal combinations of primer pairs for PCR primer multiplexing. Primer compatibility is tested against each other as well as against each other's products. Additionally, the Genome Test is performed with all possible PCR primer pairs in each multiplex group. This avoids appearance of unwanted PCR products from multiplexed groups.

6. ChipTester^TM - for testing SNP technological mutual suitability for APEX

The software controls the technological mutual suitability of different SNPs that are need be analysed on one chip, substitute SNPs which APEX primers can interact with PCR product of another SNP. 

At the moment we provide it as service.

THE SOFTWARE PACKAGE CAN BE PURCHASED IN DIFFERENT FORMS

1. One computer from Your lab will get access for 6 months to our server to perform calculations on the ASPER server through internet

2. Software will be installed locally, in Your lab. A server with our software can be accessed from any computer in local intranet with web browser

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Tel. (33) (0) 4 70 03 73 06 - interbiotech@interchim.com - http://www.interchim.com