Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database

• Published in: TheScientificWorld Vol. 2014; no. 2014; pp. 1 - 9
• Main Authors: Hill, David R. C., Mahul, Antoine, Denonfoux, Jérémie, Cipière, Sébastien, Parisot, Nicolas, Missaoui, Mohieddine, Peyretaillade, Eric, Jaziri, Faouzi, Peyret, Pierre
• Format: Journal Article
• Language: English
• Published: Cairo, Egypt Hindawi Publishing Corporation 01.01.2014; John Wiley & Sons, Inc; Hindawi Limited
• Subjects: Algorithms; Arrays; Biodiversity; Computational Biology - methods; Computer Science; Databases, Nucleic Acid; Design; Design and construction; Distributed, Parallel, and Cluster Computing; Engineering design; Equipment and supplies; Genes; Genes, rRNA; Genetics; Identification and classification; Life Sciences; Methods; Microbial activity; Microorganisms; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Probes; Organisms; Phylogenetics; Phylogeny; Poa; Probes; Probes (Electronic instruments); Quantitative Methods; RNA sequencing; Software; Systematics, Phylogenetics and taxonomy; Taxonomy; France
• ISSN: 2356-6140; 1537-744X; 1537-744X
• DOI: 10.1155/2014/350487

Phylogenetic Oligonucleotide Arrays (POAs) were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way. POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning. However, the selection of probes remains a very difficult task. The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design. Consequently, the use of high performance computing facilities is mandatory. In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids. We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI). We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous design due to bad sequence affiliation. We present here the performance and statistics of our method on real biological datasets based on a phylogenetic prokaryotic database at the genus level and a complete design of about 20,000 probes for 2,069 genera of prokaryotes.