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Nucleic Acids Research Advance Access originally published online on May 14, 2008
Nucleic Acids Research 2008 36(Web Server issue):W97-W103; doi:10.1093/nar/gkn280
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W97-W103
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

AsiDesigner: exon-based siRNA design server considering alternative splicing

Young-Kyu Park1,2, Seong-Min Park1, Young-Chul Choi3, Doheon Lee2, Misun Won1 and Young Joo Kim1,*

1Medical Genomics Research Center, KRIBB, Daejeon 305-806, 2Department of Bio and Brain Engineering, KAIST, Daejeon 305-701 and 3Bioneer, 49-3 Moonpyung-dong, Daedok, Daejeon 306-220, Korea

*To whom correspondence should be addressed. Tel: +82 42 879 8118; Fax: +82 42 879 8119; Email: yjkim8{at}kribb.re.kr

Received January 31, 2008. Revised April 22, 2008. Accepted April 26, 2008.

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/.


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