Selecting optimum DNA oligos for microarrays

Fugen Li, G. D. Stormo

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

6 Scopus citations

Abstract

High-density DNA oligonucleotide microarrays are widely used in biomedical research. In this paper, we describe algorithms to optimize the selection of specific probes for each gene in an entire genome. Having optimized probes for each gene is valuable for two reasons: (1) by minimizing background hybridization, they provide more accurate determinations of true expression levels, and (2) having optimum probes eliminates the need for multiple probes per gene, as is usually done now, thereby decreasing the cost of each microarray and increasing their usage. The criteria for truly optimum probes is easily stated, but they are not computable at present. We have developed a heuristic approach that is efficiently computable and should provide a good approximation to the true optimum set. We have run the program on the complete genomes for several model organisms and deposited the results in a database that is available online ('http://ural.wustl.edu/~lif/probe.pl').

Original languageEnglish
Title of host publicationProceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages200-207
Number of pages8
ISBN (Electronic)0769508626, 9780769508627
DOIs
StatePublished - Jan 1 2000
EventIEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000 - Arlington, United States
Duration: Nov 8 2000Nov 10 2000

Publication series

NameProceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000

Conference

ConferenceIEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000
Country/TerritoryUnited States
CityArlington
Period11/8/0011/10/00

Keywords

  • Bioinformatics
  • Cost function
  • DNA
  • Databases
  • Genetics
  • Genomics
  • Organisms
  • Probes
  • RNA
  • Sequences

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