AsiDesigner: exon-based siRNA design server considering alternative splicing.
RNA interference (RNAi) with small interfering RNA (siRNA) has become a powerful tool in functional and medical genomic research through directed post-transcriptional 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/.
Park
Young-Kyu
YK
Medical Genomics Research Center, KRIBB, Daejeon 305-806, Korea.
Park
Seong-Min
SM
Choi
Young-Chul
YC
Lee
Doheon
D
Won
Misun
M
Kim
Young Joo
YJ
D000465:Algorithms; D017398:Alternative Splicing; D020407:Internet; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry; D034741:RNA, Small Interfering / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
D012333:RNA, Messenger; D034741:RNA, Small Interfering