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iRNAchek™

RNA interference, described by Science as breakthrough of the
year, is one of the most powerful molecular biology tools, with a wide variety of applications. RNA interference is silencing of a gene caused by the introduction of a homologous dsRNA. The success of RNA interference experiment is heavily dependent on the design of short interfering RNA, for efficiency and specificity.

iRNAchek™ provides a comprehensive and intuitively designed environment for organization of sequence data, design of siRNAs, and tracking and analysis of successful templates.

Search based on specific region
iRNAchek™ provides a facility to design the siRNA based on the regions of interest. These regions can be set based on Open Reading Frames, introns, exons, UTR regions and other sequence annotations. There is also a provision to eliminate templates from specific regions.

Motif Search
It is very essential to design siRNA targets that do not fall within functionally significant motifs and domains of the sequence. iRNAchek™ takes care of this efficiently by the use of a filter to refine the results based on Motif and Domain search.

Hairpin Loop search
Efficiency of siRNA is sometimes affected by existence of stable hairpin loops. This tool identifies all possible hairpin loop formations and sorts them on the basis of their stabilization energy. User has an option to filter siRNA's overlapping with selected hairpin loops.

Statistical Analysis
iRNAchek™ has a unique tool that keeps track of successful templates and uses statistical techniques to convert the information contained in siRNA fragments into knowledge. This tool helps the user to design targets with better efficacy.

BLAST Tool
iRNAchek™ helps the user select specific siRNA's using intuitively designed BLAST tool. Using this tool the user can search for potential matches from NCBI database or can create his own proprietary database and search for matches against proprietary databases for possible matches.

Chemical Modifications
iRNAchek™ allows users to enhance siRNAs by allowing the user to define an implement chemical modification rules. The user can change overhang length, vary bases of overhangs to include deoxy bases, modify the molecule backbone, sugar groups, individual nucleotide bases including terminal bases and further. These modifications may be applied by position, by base, and by strand.

siRNA library
iRNAchek™ provides a user a library to store designed siRNA templates, along with any modification done. A set of siRNA selection filters, are given to the user for enabling performance analysis.

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