RNAbor: a web server for RNA structural neighbors
2007 (English)In: Nucleic Acids Research, ISSN 0305-1048, Vol. 35, no Suppl. S: Web Server issue, W305-W309 p.Article in journal (Refereed) Published
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 d base pairs. For each distance delta RNAbor computes the density of delta-neighbors, the number of delta-neighbors, and the MFE structure, or MFEd 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.
Place, publisher, year, edition, pages
2007. Vol. 35, no Suppl. S: Web Server issue, W305-W309 p.
Cluster Analysis, Computational Biology/*methods, Computer Simulation, Conserved Sequence, Databases, Genetic, Internet, Molecular Sequence Data, Nucleic Acid Conformation, RNA/*chemistry, RNA, Untranslated, Regulatory Sequences, Ribonucleic Acid, Sequence Alignment, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid
IdentifiersURN: urn:nbn:se:uu:diva-96426DOI: 10.1093/nar/gkm255ISI: 000255311500057PubMedID: 17526527OAI: oai:DiVA.org:uu-96426DiVA: diva2:170995