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.

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We thank Drs Jude Onyia, Eric Su and Birong Liao for their support and critical review. The research reported in this paper was supported in part by National Science Foundation (NSF) Information Technology Research (ITR) grant number NSF-IIS/ITR 0081944, a National Institutes of Health (NIH) BISTI (Biomedical Information Science and Technology Initiative) grant, and NIH-NIGMS (National Institute of General Medical Sciences) grant number P20 GM66402.

The authors have no conflicts of interest that are directly relevant to the content of this article.

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Correspondence to Dr Shuyu Li.

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Availability: 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.

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Mamidipalli, S., Palakal, M. & Li, S. OligoMatcher. Appl-Bioinformatics 5, 121–124 (2006). https://doi.org/10.2165/00822942-200605020-00008

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  • Oligonucleotide Sequence
  • Affymetrix Oligonucleotide Array
  • Oligonucleotide Array Data
  • Effective siRNA Sequence
  • Optimal Oligonucleotide