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CJ Chen, N Servant, J Toedling, A Sarazin, A Marchais, E Duvernois-Berthet, V Cognat, V Colot, O Voinnet, E Heard, C Ciaudo and E Barillot
Abstract
SUMMARY: ncPRO-seq (Non-Coding RNA PROfiling in sRNA-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on small RNAs 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 small RNAs. It also has a module to identify regions significantly enriched with short reads, that cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or 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 small RNA raw data from the 3 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; cciaudo@ethz.chSupplementary information Supplementary data are available at Bioinformatics online.
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Concepts
Ribosomal RNA, Small interfering RNA, Xist, Long noncoding RNA, Transfer RNA, Non-coding RNA, DNA, RNA
MeSH headings
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