title: Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases.
abstract: Large-scale transcriptome projects have shown that the number of RNA transcripts not coding for proteins (non-coding RNAs) is much larger than previously recognized. High-throughput technologies, coupled with bioinformatics approaches, have produced increasing amounts of data, highlighting the role of non-coding RNAs (ncRNAs) in biological processes. Data generated by these studies include diverse non-coding RNA classes from organisms of different kingdoms, which were obtained using different experimental and computational assays. This has led to a rapid increase of specialized RNA databases. The fast growth in the number of available databases makes integration of stored information a difficult task. We present here NRDR, a Non-coding RNA Databases Resource for information retrieval on ncRNA databases (www.ncrnadatabases.org). We performed a survey of 102 public databases on ncRNAs and we have introduced four categorizations to classify these databases and to help researchers quickly search and find the information they need: RNA family, information source, information content and available search mechanisms. NRDR is a useful databases searching tool that will facilitate research on ncRNAs.
authors.affiliation: Engenharia da Computação, Universidade Tecnológica Federal do Paraná-Campus Cornélio Procópio, Cornélio Procópio, Brazil.
authors.forename: Alexandre Rossi
authors.initials: AR
authors.lastname: Paschoal
authors.forename: Vinicius
authors.initials: V
authors.lastname: Maracaja-Coutinho
authors.forename: João Carlos
authors.initials: JC
authors.lastname: Setubal
authors.forename: Zilá Luz Paulino
authors.initials: ZL
authors.lastname: Simões
authors.forename: Sergio
authors.initials: S
authors.lastname: Verjovski-Almeida
authors.forename: Alan Mitchell
authors.initials: AM
authors.lastname: Durham
mesh_terms: D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D020407:Internet; D058977:Molecular Sequence Annotation; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D022661:RNA, Untranslated