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


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


BACKGROUND
sqwang@nic.bmi.ac.cn.
Bo
Xiaochen
X
Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China.
Wang
Shengqi
S
D000465:Algorithms; D003196:Computer Graphics; D018390:Gene Targeting / Q000379:methods*; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D016376:Oligonucleotides, Antisense; D012333:RNA, Messenger