Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 75005 Paris, France.
Nucleic Acids Res. 2010 Jun;38(10):e117. doi: 10.1093/nar/gkq110. Epub 2010 Feb 21.
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/.
尽管新的高通量测序技术不断发展，但微阵列仍然是研究小基因组生物的有吸引力的工具，这要归功于样品的多路复用和高密度的特征。然而，寡核苷酸设计对于大多数用户来说仍然是一个微妙的步骤。有大量的软件可用于解决这个问题，但每个程序都是用自己的策略开发的，这使得选择最佳解决方案变得困难。在这里，我们描述了 Teolenn，这是一个通用的探针设计工作流程，具有灵活和可定制的模块组织，允许生成固定或可变长度的寡核苷酸。此外，我们的软件能够为每个设计的探针提供质量评分。为了评估这些评分的相关性，我们使用针对里氏木霉真菌基因组设计的平铺阵列进行了真实的杂交。我们表明，我们的评分管道与所有设计探针的信号质量相关，对于 97.2%的探针都可以进行质量评分和信号强度之间的后验比较。这一结果有助于在设计步骤中丢弃任何不良评分的探针，以获得高质量的微阵列。Teolenn 可在 http://transcriptome.ens.fr/teolenn/ 上获得。
