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

Bioinformatics. 2005 Apr 15;21(8):1401-2. doi: 10.1093/bioinformatics/bti211. Epub 2004 Dec 14.


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


Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computer Graphics
  • Gene Targeting / methods*
  • Nucleic Acid Conformation
  • Oligonucleotides, Antisense / genetics*
  • RNA, Messenger / genetics*
  • Sequence Alignment / methods*
  • Sequence Analysis, RNA / methods*
  • Software*
  • User-Computer Interface*


  • Oligonucleotides, Antisense
  • RNA, Messenger