title: NAPP: the Nucleic Acid Phylogenetic Profile Database.
abstract: Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.
authors: Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, bâtiment 400, 91405 Orsay Cedex, France.
authors: Alban
authors: A
authors: Ott
authors: Anouar
authors: A
authors: Idali
authors: Antonin
authors: A
authors: Marchais
authors: Daniel
authors: D
authors: Gautheret
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D010802:Phylogeny; D019642:RNA, Archaeal / Q000145:classification / Q000235:genetics*; D012329:RNA, Bacterial / Q000145:classification / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid