title: ptRNApred: computational identification and classification of post-transcriptional RNA.
abstract: Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences coding for post-transcriptional RNA from the genomic sequence with an overall sensitivity of 91% and a specificity of 94% and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA.
  
  
  BACKGROUND
  The ptRNApred software is open for public use on http://www.ptrnapred.org/.
authors.affiliation: Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany.
authors.forename: Yask
authors.initials: Y
authors.lastname: Gupta
authors.affiliation: Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany mareike.witte@medizin.uni-luebeck.de.
authors.forename: Mareike
authors.initials: M
authors.lastname: Witte
authors.affiliation: Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Möller
authors.affiliation: Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany.
authors.forename: Ralf J
authors.initials: RJ
authors.lastname: Ludwig
authors.affiliation: Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Restle
authors.affiliation: Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Zillikens
authors.affiliation: Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany saleh.ibrahim@uk-sh.de.
authors.forename: Saleh M
authors.initials: SM
authors.lastname: Ibrahim
mesh_terms: D019295:Computational Biology / Q000379:methods; D005786:Gene Expression Regulation; D022661:RNA, Untranslated / Q000737:chemistry / Q000145:classification*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D060388:Support Vector Machine
chemical_list: D022661:RNA, Untranslated