Whole Genome Scale Oligo Design
Using Sarani, thousands of gene sequences can be analyzed together and optimal oligo probes with uniform thermodynamic properties can be designed. (See examples of whole genome oligo designs using Sarani).

Store-and-Query Paradigm
Sarani computes and builds a database of all possible oligonucleotide probes for all genes at broad parameter settings. Though this is a computation intensive step, the oligo database has to be built only once and contains comprehensive hybridization information for all potential probes. Subsequently, the user can query the database and retrieve optimal oligo probes specified by the desired parameters. This allows for greater efficiency and accuracy as the right parameters are typically not evident a priori and a change of parameters only calls for a new fast query as opposed to expensive recomputation of the hybridization parameters

Parameter Optimization
Probes which can go on to a microarray need to satisfy several properties, e.g., have the right melting temperatures, have specificity to the genes they are meant for, have no secondary structure effects which prevent hybridization etc. Thus finding optimal probes involves optimization over a multi-parameter space. Sarani facilitates multiparameter optimization through interfaces which facilite filtering based on several parameters which affect hybridization and ranking probes which pass the filtering step based on pre-defined or user-defined functions. In addition, the interface also provides hints on which parameters are too tight and need to be relaxed.

Cross-Hybridization Simulation
Specificity of oligonucleotide probes is computed not based on sequence similarity alone, but based on extensive cross hybridization simulations. An fast and proprietary BLAST like sequence similarity search algorithm has been integrated into Sarani; this algorithm finds and measures alignments based on not just homology but on the predicted hybridization strength. The hybridization strength for both perfect complementary alignments and non-specific alignments is quantified by a DNA melting temperature computed using hybridization thermodynamic parameters available in scientific literature.

Secondary Structure Effects
Oligonucleotide probes containing self-complementary regions that are likely to form secondary structures are avoided, as are probes which lie in non-exposed regions of the target gene.

Low Complexity Masking
Low complexity regions in the target gene sequences are masked out and oligonucleotide probes in such regions are avoided.

Interactive Graphical User Interface
Sarani has interactive user interface (GUI) and all steps in the oligo design process can be executed with only a few mouse clicks. Various features of Sarani like Preview (which gives a quick preview of how many genes have probes satisfying the currently chosen parameters) and Iterative Query (which allows the user to choose tight parameters, find probes for as many genes as possible using these parameters, and then relax the parameters to satisfy more genes) aid in the selection of overall tight parameters and allow selection of good quality oligonucleotide probes for all genes. Properties of chosen oligos are then displayed in SpreadSheet tables that allow graphical visualization and manipulation.

Sequence Formats
Sarani can read reference and target sequences in the commonly used FASTA sequence format.

System Details
Available as a Desktop or a Client-Server version on Windows, Linux and other flavours of Unix. Minimum memory required 256MB, recommended 1GB. A Relational Database (either Oracle or MySql) running on either the same machine or another machine on the LAN is needed.