OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W611-5. doi: 10.1093/nar/gki399.

Abstract

OligoWiz 2.0 is a powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition to probe selection according to a series of probe quality parameters, cross-hybridization, T(m), position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management. Furthermore, we show that probes designed using OligoWiz 2.0 give rise to consistent hybridization results (http://www.cbs.dtu.dk/services/OligoWiz2).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Gene Expression Profiling / methods*
  • Internet
  • Nucleic Acid Conformation
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Probes / chemistry*
  • Reproducibility of Results
  • Sequence Analysis, RNA / methods*
  • Software*
  • Systems Integration
  • User-Computer Interface

Substances

  • Oligonucleotide Probes