title: ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  Source code, annotation files, manual and online version are available at http://ncpro.curie.fr/.
  
  
  BACKGROUND
  bioinfo.ncproseq@curie.fr or cciaudo@ethz.ch
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institut Curie, F-75248 Paris, France. bioinfo.ncproseq@curie.fr
authors.forename: Chong-Jian
authors.initials: CJ
authors.lastname: Chen
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.forename: Joern
authors.initials: J
authors.lastname: Toedling
authors.forename: Alexis
authors.initials: A
authors.lastname: Sarazin
authors.forename: Antonin
authors.initials: A
authors.lastname: Marchais
authors.forename: Evelyne
authors.initials: E
authors.lastname: Duvernois-Berthet
authors.forename: Valérie
authors.initials: V
authors.lastname: Cognat
authors.forename: Vincent
authors.initials: V
authors.lastname: Colot
authors.forename: Olivier
authors.initials: O
authors.lastname: Voinnet
authors.forename: Edith
authors.initials: E
authors.lastname: Heard
authors.forename: Constance
authors.initials: C
authors.lastname: Ciaudo
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D034741:RNA, Small Interfering / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D034741:RNA, Small Interfering; D022661:RNA, Untranslated