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ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data

Chen, Chong-Jian ; Servant, Nicolas ; Toedling, Joern ; Sarazin, Alexis ; Marchais, Antonin ; Duvernois-Berthet, Evelyne ; Cognat, Valérie ; Colot, Vincent ; Voinnet, Olivier ; Heard, Edith ; Ciaudo, Constance ; Barillot, Emmanuel

In: Bioinformatics, 2012, vol. 28, no. 23, p. 3147-3149

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    Title
    • ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data
    Author
    • Chen, Chong-Jian. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Servant, Nicolas. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Toedling, Joern. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Sarazin, Alexis. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Marchais, Antonin. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Duvernois-Berthet, Evelyne. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Cognat, Valérie. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Colot, Vincent. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Voinnet, Olivier. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Heard, Edith. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Ciaudo, Constance. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    • Barillot, Emmanuel. Institut Curie, CNRS UMR3215, INSERM U934, INSERM U900, F-75248 Paris, France, Mines ParisTech, F-77300 Fontainebleau, France, Institute of Molecular Biology gGmbH, G-55128 Mainz, Germany, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, and INSERM U1024, F-75248 Paris, France, Department of Biology, Swiss Federal Institute of Technology, Department of Biology, S-8092 Zurich, Switzerland and Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, F-67084 Strasbourg, France
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:296018
    Summary
    Summary: Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions. The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that sRNA raw data from the three current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) can be analyzed with this pipeline. The ncPRO-seq pipeline can be used to analyze read and alignment data, based on any sequenced genome, including mammals and plants. Availability: Source code, annotation files, manual and online version are available at http://ncpro.curie.fr/. Contact: bioinfo.ncproseq@curie.fr or cciaudo@ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online