1. Can I design oligos for the entire genome i.e., for all the gene sequences of a species?
Yes, using Sarani you can design optimal oligonucleotide probes for all the gene sequences of a species. For some examples of whole genome oligo designs please refer Sarani case studies.
2. Can I design oligos for a subset of gene sequences of a species?
Yes, you can design oligos for all or a subset of gene sequences of a species.
3. Can I design oligos of different lengths at the same run?
Yes, the user can design oligos of various lengths in the same run. The desired range of oligo lengths and the step by which the lengths need to be incremented can be specified during oligo design step.
4. What format the gene sequences be input to Sarani?
Sarani requires sequence databases to be in FASTA (Pearson) Format. A single file may contain one or many sequences in FASTA format.
 5. What is an Oligo Database?
Oligo Database is a database of all possible oligo probes computed for all genes in a target sequence database. For each oligo, SARANI computes various properties relevant to its sensitivity (e.g. melting temperature, GC content, self complementarity score), and specificity (cross hybridization possibilities) and stores in a Relational Database. Once oligo database is computed the user can interactively retrieve optimal oligo probes suitable for specific conditions.
6. Why do I need a Oligo Database?
Genome scale oligo design is a computationally intensive process. If the oligo selection criteria are specified at the begining of this computation, at the end of the process the user may find that some of the selected probes are not suitable for experiments. Then the user has to change selection parameters and initiate the time consuming oligo design process again. To avoid frequent oligo computation and to make the selection process more interactive, SARANI employes a novel Oligo Database approach. During initial oligo design process, the user specifies a set of broad parameter conditions and then SARANI computes all possible oligos for all gene sequences along with their properties and stores in a relational database. Though this is time consuming step, the user has to compute the oligo database for only one time. Once the oligo database is built, the user can interactively query the database, view oligo probe properties and select good quality probes for specific experimental conditions.
7. How does Sarani selects optimal oligonucleotide probes?
In Sarani, selection of optimal oligonucleotide probes occurs at two levels.
(1) In the first filtering stage, based on the parameters specified by the user, for each of the target gene sequence Sarani sends queries to the Oligo Database and retrives only those probes that satisfy given conditions.
(2) In the second ranking stage, Sarani ranks the filtered oligonucleotide probes based on their properties using user specified ranking function and then selects the probes with highest ranks as most optimal oligonucleotide probes.
8. What are hardware requirements for running Sarani?
A desktop PC with the following configuration is minimum. Intel P4
(or equivalent AMD) 1GHz CPU, 256MB RAM and 4GB of disk space. However, recommended configuration would be any processor running 1.5GHz and above, 512MB RAM and several GB of disk space.
9. What platforms are supported?
Windows NT 4.0, Windows 2000, Windows XP, Linux (Debian, Redhat7.2) are supported.
10. What databases are supported?
Sarani supports Oracle and MySql relational databases.
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