chipD: A web tool to design oligonucleotide probes for high-density tiling arrays

Yann S. Dufour, Gary E. Wesenberg, Andrew J. Tritt, Jeremy D. Glasner, Nicole T. Perna, Julie C. Mitchell, Timothy J. Donohue

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences, a set of parameters that allow probe design to be tailored to specific applications, protocols or the array manufacturer's requirements. The algorithm optimizes probes to meet three objectives: (i) probes should be specific; (ii) probes should have similar thermodynamic properties; and (iii) the target sequence coverage should be homogeneous and avoid significant gaps. The output provides in a text format, the list of probe sequences with their genomic locations, targeted strands and hybridization characteristics. chipD has been used successfully to design tiling arrays for bacteria and yeast. chipD is available at http://chipd.uwbacter.org/.

Original languageEnglish
Article numbergkq517
Pages (from-to)W321-W325
JournalNucleic Acids Research
Volume38
Issue numberSUPPL. 2
DOIs
StatePublished - Jun 5 2010
Externally publishedYes

Funding

Department of Energy Genome to Life BACTER (grants ER63232-1018220-0007203 and DE-FG02-05ER15653 to Y.S.D.); UW-Madison College of Agricultural and Life Sciences (Wisconsin Distinguished Graduate Fellowship to Y.S.D.); UW-Madison Department of Bacteriology (William H. Peterson Predoctoral Fellowship to Y.S.D.); National Institutes of Health (R01-GM62994 to N.T.P., A.J.T.); National Institutes of Health (GM075273 to T.J.D.); UW-Madison Draper Technology Innovation Fund (to T.J.D.). Funding for open access charge: National Institutes of Health (GM075273).

FundersFunder number
UW-Madison
UW-Madison Department of Bacteriology
National Institutes of HealthGM075273
National Institute of General Medical SciencesR01GM062994
College of Agricultural and Life Sciences

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