Teolenn: An efficient and customizable workflow to design high-quality probes for microarray experiments

Laurent Jourdren, Aurélie Duclos, Christian Brion, Thomas Portnoy, Hugues Mathis, Antoine Margeot, Stéphane Le Crom

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/.

Original languageEnglish (US)
Article numbergkq110
Pages (from-to)e117
JournalNucleic acids research
Volume38
Issue number10
DOIs
StatePublished - Feb 20 2010

Fingerprint Dive into the research topics of 'Teolenn: An efficient and customizable workflow to design high-quality probes for microarray experiments'. Together they form a unique fingerprint.

Cite this