Filtering : In the first step, probes which do not satisfy the chosen parameter settings for this iteration are filtered away using a database query. This step helps in ensuring uniform thermodynamic and other specificity related properties for all oligonucleotide probes selected in this iteration.

Ranking: In this second step, all oligonucleotide probes retrieved for a gene sequence (and satisfying the filtering parameters above) are ranked so the best few can be chosen. Sarani has three predefined ranking functions. In addition, it provides a wizard which allows construction of an Advanced Ranking Function taking user-weighted combinations of various parameters.