Array Designer

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Microarray Software

Oligonucleotides are finding greater use as they are printed as DNA Microarrays.

Applications include:
Clone mapping
Deletion studies
Gene expression
Gene mapping
Gene re-sequencing
SNP analysis

For this reason, TeleChem International, Inc. and PREMIER Biosoft International have joined forces to make state-of-the-art oligonucleotide design software available to the researcher at an affordable price.

Don’t pay large upfront costs to bioinformatics companies that will not allow you to own your sequences and discoveries!

There are two ways to get your oligo’s designed for your arrays:

1. Buy the Array Designer Software for only $4,885.00 (Catalog# ADS3)
OR
2. Hire TeleChem/arrayit.com for $20.00 per oligo.

For a FREE demo, click here.

Please write to us if you would like to evaluate the program using your own sequences:
http://www.premierbiosoft.com/jsp/customer/RequestEvaluation.jsp

TeleChem International, Inc. Oligo Design Directive Steps 1-8.

1. Select 60-mers from any organism of choice
2. Oligos should also include the appropriate controls (i.e. different organism).
3. All oligos should map to the 3' end of cDNAs
4. All oligos should map to within 1,000 nt of the 3' cDNA end
5. All oligos should correspond to the coding strand (protein strand)
6. Avoid sequence repeats and stretches of polyA, G, C and T
7. Avoid extremes of Tms (mixed sequence composition best)
8. Run against the database to avoid cross-reactivity (<70% sequence identity). “Blast Button"

PCR Primer and Probe Design

Automatic Homology Avoidance- Hundreds of sequences are BLAST searched. The results are automatically interpreted and the homologies identified are avoided during the design

Specificity check- The primers and probes designed by the program can be BLAST searched against all the nucleotide databases available at NCBI to verify the specificity of design.

Product Location- Allows specifying the product length and product location viz at the 3’end, 5’end or anywhere in the sequence.

Comprehensive selection criteria- Screens oligos for their thermodynamic properties as well as secondary structures. Graphics for the structures are also displayed.

Ranking- Uses statistical optimization techniques to design the best primer and probe for each template. A list of alternate designs is also available.

Algorithm- Calculates oligo Tm using the highly accurate SantaLucia nearest neighbor thermodynamic values.

Multiple probes- Designs multiple probes per sequence for increased accuracy of detection.
Allows specifying the minimum distance between two probes to avoid overlapping.

SNP detection- Designs probes to span the site. Designs both wild and mutant probes.

SNP detection with primer extension- Designs probes located with their 3’end at the specified site.

cDNA oligonucleotide array- Designs probes to be located anywhere within a region around the site. Allows design of multiple probes near the 3' end of the sequence for redundant cDNA detection.

BLAST

Specificity Check- Thousands of searches are submitted automatically. Results interpreted and are displayed in the Homology Avoidance window.

Oligo and Amplicon BLAST- The oligos designed by the program and the amplicon can be BLAST searched against any or all of the nucleotide databases available at NCBI.

Uniform conditions- PCR primer design is optimized to amplify all sequences under uniform reaction conditions.

Custom databases- Works with custom databases saved locally using standalone WWW BLAST facility of NCBI.

Repeat regions- Optimizes BLAST search parameters to detect human repeats while searching the human RNA (previously called mRNA) database at NCBI.

Speed

Per sequence- Processes a 10kb sequence in 2-3 seconds.

10 minutes- Processor approximately 300 10kb sequences in 10 minutes.

Data management

Application Database- Maintains a local database for sequence information and BLAST results.

Data management- Manages data of multiple users and multiple projects by creating a separate project for each.

Input / Output

File formats- Supports GenBank and FastA formats. GenBank and FastA formatted files can contain multiple sequences.

Unlimited templates- Supports any number of templates in a single run.

Flexible output format- Outputs a tab delimited format ready for viewing and manipulating in any spread sheet program, or databases like Oracle or Access; or in synthesis order forms of a vendor of your choice.

Specify output- Allows control over primer and probe properties that are to be exported to the output file.

SNP specific Primer and Oligo Probe Design

SNP loading- easily add a single SNP at a time or load thousands of SNPs using standard GenBank variation files.

SNP detection- designs SNP probes for both hybridization and primer extension detection PCR Primers.

SNP amplification- designs primers to amplify SNP sites.

Array Designer 3 FAQ:

1. What is the maximum number of oligos that can be designed? Can it design 10,000?

Yes, this can be done in just a few hours. We have many customers doing 20,000 or more sets. To design highly specific probes using Array Designer, we recommend first BLASTing the sequences. BLASTing sequences in batches of 200 is advisable for optimum utilization of a system's resources. A BLAST search against a local database should take about 7-8 min. This can be even faster depending on the speed of the local server. You are now ready to run a probe search on your sequences. Array Designer may take up to two hours to analyze and save results while processing 15,000 sequences in a single run using the "Avoid Cross Homology" option. For faster analysis we suggest working with 5000 sequences at a time. Array Designer will take about 25-30 minutes to process a batch of 5000. Our calculations were made on a Pentium III 650MHz machine with 192MB RAM.

2. What is the maximum length oligo that can be designed.

Array Designer can design both long and short oligos for expression and SNP genotyping microarrays. Though up to 99bp long probes can be designed, built-in design parameters are available for 18 to 75 mers.

3. Are there plans for a version to run on Linux and Macintosh?

Yes, Array Designer 3.00 is also available for Linux and Macintosh.

For details, please visit: http://www.premierbiosoft.com/products/system_requirements/system_requirements.html

Order Information

Product

Description

Catalog I.D.

Price (U.S. dollars)

Premiere Biosoft ArrayDesigner Software for Windows

Oligonucleotide design software for Windows

ADS3

$5373.50

Premiere Biosoft ArrayDesigner Software Upgrade

Oligonucleotide design software upgrade

ADU3

$2200

Click on the button below to place an order for any of our products.

***** International pricing may vary as much as 30% (or more depending on country) due to import duties, stocking fees and technical support.