DNA Microarray technology has emerged as a powerful tool for genome scale expression studies, disease gene identification, genotyping and diagnostics Oligo design process is the first and the most critical step in oligonucleotide microarray fabrication.

Sarani technology from Strand is a solution for automatic large-scale design of optimal oligonucleotide probes for microarray experiments. Sarani can be used for designing oligonucleotide probes and persisting them in a database for further analysis. It takes into account all possible overlapping oligonucleotide sequences and computes their properties in terms of specificity, sensitivity and stability when bound to target cDNA / RNA molecule and free from secondary structure). The results are stored in a database and can be queried using a convenient graphical user interface (GUI).

It is standalone technology that runs on Windows and Linux/Unix platforms. Sarani currently uses MySql as a default database to store the computed oligonucleotides, but other databases (Oracle, etc) are also supported. Sarani can also be configured to a client-server mode.

Key features of Sarani:

1. Operates at whole genome level
2. Parameters for oligo design are highly configurable
3. Unique specificity algorithm based upon hybridization thermodynamics rather than homology
4. Extensive simulation of cross hybridization effects
5. Melting temperatures and free energies of true and cross matches calculated for each probe
6. Low complexity regions masked from further analysis
7. Predicts and takes into account secondary structures formed by the probe and by the target.
8. Cross platform (Windows/ Linux/ UNIX) and works in client server mode through a GUI
9. Design results stored in a database for easy querying with various choices of parameters
10. Graphical visualization of probe properties
11. Probe data saved in compatible Excel spreadsheet
12. Sequence similarity tool (such as BLAST) developed in house is integrated with the tool
13. Online help available

Documentation

Click here for Tour of Sarani