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Bioinformatics Advance Access published online on December 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti211
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received April 25, 2004
Revised October 17, 2004
Accepted December 6, 2004

Article

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

Xiaochen Bo 1 and Shengqi Wang 1*

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

* To whom correspondence should be addressed.
Shengqi Wang, E-mail: sqwang{at}nic.bmi.ac.cn


  Abstract

Summary: TargetFinder is a PC/Windows program for interactive effective antisense oligonucleotides 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 AOs target sites selection.

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


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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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