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Bioinformatics Advance Access originally published online on December 14, 2004
Bioinformatics 2005 21(8):1401-1402; doi:10.1093/bioinformatics/bti211
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA

Xiaochen Bo and Shengqi Wang *

Beijing Institute of Radiation Medicine 27 Taiping Road, Haidian District, Beijing 100850, China

*To whom correspondence should be addressed.

Summary: TargetFinder is a PC/Windows program for interactive effective antisense oligonucleotide (AO) selection based on mRNA accessible site tagging (MAST) and secondary structures of target mRNA. To make MAST result intuitive, both the alignment result and tag frequency profile is illustrated. As theoretical reference, secondary structure and single strand probability profile of target mRNA is also represented. All of these sequences and profiles are displayed in aligned mode, which facilitates identification of the accessible sites in target mRNA. Graphical, user-friendly interface makes TargetFinder a useful tool in AO target site selection.

Availability: The software is freely available at http://www.bioit.org.cn/ao/targetfinder.htm

Contact: sqwang{at}nic.bmi.ac.cn


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This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
X. Bo, S. Lou, D. Sun, J. Yang, and S. Wang
AOBase: a database for antisense oligonucleotides selection and design
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D664 - D667.
[Abstract] [Full Text] [PDF]


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