title: RNAbor: a web server for RNA structural neighbors.
abstract: RNAbor provides a new tool for researchers in the biological and related sciences to explore important aspects of RNA secondary structure and folding pathways. RNAbor computes statistics concerning delta-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A delta-neighbor is a structure that differs from the input structure by exactly delta base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly delta base pairs. For each distance delta RNAbor computes the density of delta-neighbors, the number of delta-neighbors, and the MFE structure, or MFE (delta) structure, among all delta-neighbors. RNAbor can be used to study possible folding pathways, to determine alternate low-energy structures, to predict potential nucleation sites and to explore structural neighbors of an intermediate, biologically active structure. The web server is available at http://bioinformatics.bc.edu/clotelab/RNAbor.
authors.affiliation: Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden.
authors.forename: Eva
authors.initials: E
authors.lastname: Freyhult
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D017124:Conserved Sequence; D030541:Databases, Genetic; D020407:Internet; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA