Sarani automates large-scale design of optimal oligonucleotide probes for microarray experiments. Using Sarani, thousands of gene sequences can be analyzed together and the best available oligonucleotide probes with uniform thermodynamic properties and minimal similarity to non-specific genes can be selected. The accuracy and efficiency of the design and selection process is facilitated by new implementations of algorithms for predicting hybridization properties along with a unique store-and-query database paradigm, which allows the user to tightly control on the design parameters. Sarani is available as either a desktop or a client server version and runs on Windows, Unix and Linux.

  Key Benefits:

Whole Genome Scale Oligo Design
Design oligos for several thousand gene sequences simultaneously.

Novel Store-and-Query Paradigm
First compute properties for all potential oligos, then choose optimal oligos by querying with the appropriate parameters.

Iterative Oligo Database Querying
Keep design parameters tight and relax only if necessary. The User Interface facilitates determination of which of several parameters to relax.

Filtering on Design Parameters
Filter out probes based on several parameters affecting hybridization quality.

Oligo Ranking Functions
Several pre-defined and user-definable ranking functions to rank selected probes.

Computation of Hybridization Properties
Algorithms to compute oligo specificity based on extensive cross-hybridization simulation.

Integrated Sequence Similarity Module
A fast integrated sequence similarity module identifies alignments based on not just homology but potential for hybridization.