RNA interference (RNAi) with small interfering RNA
(siRNA) has become a powerful tool in functional and
medical genomic research through directed posttranscriptional
gene silencing. In order to apply
RNAi technique for eukaryotic organisms, where
frequent alternative splicing results in diversification
of mRNAs and finally of proteins, we need spliced
mRNA isoform silencing to study the function of
individual proteins. AsiDesigner is a web-based
siRNA design software system, which provides
siRNA design capability to account for alternative
splicing for mRNA level gene silencing. It provides
numerous novel functions including the designing of
common siRNAs for the silencing of more than two
mRNAs simultaneously, a scoring scheme to evaluate
the performance of designed siRNAs by adopting
currently known key design factors, a stepwise
off-target searching with BLAST and FASTA algorithms
and checking the folding secondary structure
energy of siRNAs. To do this, we developed a novel
algorithm to evaluate the common target region,
where siRNAs can be designed to knockdown a
specific mRNA isoform or more than two mRNA
isoforms from a target gene simultaneously. The
developed algorithm and the AsiDesigner were
tested and validated as very effective throughout
widely performed gene silencing experiments. It is
expected that AsiDesigner will play an important role
in functional genomics, drug discovery and other
molecular biological research. AsiDesigner is freely
accessible at http://sysbio.kribb.re.kr/AsiDesigner/.