title: OligoMatcher: analysis and selection of specific oligonucleotide sequences for gene silencing by antisense or siRNA.
abstract: 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).
authors.affiliation: Department of Computer and Information Science, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana, USA.
authors.forename: SudhaRani
authors.initials: S
authors.lastname: Mamidipalli
authors.forename: Mathew
authors.initials: M
authors.lastname: Palakal
authors.forename: Shuyu
authors.initials: S
authors.lastname: Li
mesh_terms: 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
chemical_list: D009841:Oligonucleotides; D016376:Oligonucleotides, Antisense; D034741:RNA, Small Interfering