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Title 

AsiDesigner: exon-based siRNA design server considering alternative splicing

Authors 

Young-Kyu ParkSeong Min ParkY C ChoiD LeeMi Sun WonYoung Joo Kim

Publisher 

Oxford University Press

Issue Date 

2008

Citation 

Nucleic Acids Research, vol. 36, no. Sup 2, pp. w97-w103

Keywords 

alternative RNA splicingalternative splicing

Abstract 

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.

ISSN 

0305-1048

Link 

http://dx.doi.org/10.1093/nar/gkn280

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2017-04-19


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