OligoMatcher: analysis and selection of specific oligonucleotide sequences for gene silencing by antisense or siRNA.
OligoMatcher is a web-based tool for analysis and selection of unique oligonucleotide sequences for gene silencing by antisense oligonucleotides (ASOs) or small interfering RNA (siRNA). A specific BLAST server was built for analysing sequences of ASOs that target pre-mRNA in the cell nucleus. Tissue- and cell-specific expression data of potential cross-reactive genes are integrated in the OligoMatcher program, which allows biologists to select unique oligonucleotide sequences for their target genes in specific experimental systems.


BACKGROUND
The OligoMatcher web server is available at http://shelob.cs.iupui.edu:18081/oligomatch.php. The source code is freely available for non-profit use on request to the authors.


BACKGROUND
Mathew Palakal (mpalakal@cs.iupui.edu) or Shuyu Li (li_shuyu_dan@lilly.com).
Mamidipalli
SudhaRani
S
Department of Computer and Information Science, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana, USA.
Palakal
Mathew
M
Li
Shuyu
S
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020868:Gene Silencing; D006801:Humans; D020407:Internet; D009841:Oligonucleotides / Q000737:chemistry*; D016376:Oligonucleotides, Antisense; D034741:RNA, Small Interfering; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
D009841:Oligonucleotides; D016376:Oligonucleotides, Antisense; D034741:RNA, Small Interfering