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Nucleic Acids Research Advance Access originally published online on February 10, 2009
Nucleic Acids Research 2009 37(6):1726-1739; doi:10.1093/nar/gkp053
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Nucleic Acids Research, 2009, Vol. 37, No. 6 1726-1739
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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An evaluation of custom microarray applications: the oligonucleotide design challenge

Sophie Lemoine1,2,3, Florence Combes1,2 and Stéphane Le Crom1,2,3,*

1INSERM, CNRS, IFR36, Plate-forme Transcriptome, 2École normale supérieure and 3INSERM, U784, 46 rue d’Ulm, 75230 Paris Cedex 05, France

*To whom correspondence should be addressed. Tel: +33 1 44 32 23 72; Fax: +33 1 44 32 39 88; Email: lecrom{at}biologie.ens.fr

Received October 17, 2008. Revised January 9, 2009. Accepted January 19, 2009.

The increase in feature resolution and the availability of multipack formats from microarray providers has opened the way to various custom genomic applications. However, oligonucleotide design and selection remains a bottleneck of the microarray workflow. Several tools are available to perform this work, and choosing the best one is not an easy task, nor are the choices obvious. Here we review the oligonucleotide design field to help users make their choice. We have first performed a comparative evaluation of the available solutions based on a set of criteria including: ease of installation, user-friendly access, the number of parameters and settings available. In a second step, we chose to submit two real cases to a selection of programs. Finally, we used a set of tests for the in silico benchmark of the oligo sets obtained from each type of software. We show that the design software must be selected according to the goal of the scientist, depending on factors such as the organism used, the number of probes required and their localization on the target sequence. The present work provides keys to the choice of the most relevant software, according to the various parameters we tested.

Present address: Combes Florence, CEA, IRTSV, LBIM, 38054 Grenoble, France

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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