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Appl Bioinformatics. 2006;5(2):121-4.

OligoMatcher: analysis and selection of specific oligonucleotide sequences for gene silencing by antisense or siRNA.

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  • 1Department of Computer and Information Science, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana, USA.


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.


The OligoMatcher web server is available at The source code is freely available for non-profit use on request to the authors.


Mathew Palakal ( or Shuyu Li (

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