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Literature DB >> 12824351

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.

Henrik Bjørn Nielsen¹, Rasmus Wernersson, Steen Knudsen.

Abstract

Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added to the program to extend the default parameters: homology, DeltaTm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/.

Entities: Chemical Gene

Mesh：

Substances：
DNA Primers

Year: 2003 PMID： 12824351 PMCID： PMC169028 DOI： 10.1093/nar/gkg622

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

11 in total

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3. Selection of optimal DNA oligos for gene expression arrays.

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10. Oligodb--interactive design of oligo DNA for transcription profiling of human genes.

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46 in total

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Authors: T Majtán; G Bukovská; J Timko
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Authors: T J Gentry; G S Wickham; C W Schadt; Z He; J Zhou
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6. Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data.

Authors: Luisa A Marcelino; Vadim Backman; Andres Donaldson; Claudia Steadman; Janelle R Thompson; Sarah Pacocha Preheim; Cynthia Lien; Eelin Lim; Daniele Veneziano; Martin F Polz
Journal: Proc Natl Acad Sci U S A Date: 2006-09-01 Impact factor: 11.205