Boltzmann probability of RNA structural neighbors and riboswitch detection
2007 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 23, no 16, 2054-2062 p.Article in journal (Refereed) Published
Motivation: We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure.
Results: A secondary structure of s is called a -neighbor of if and differ by exactly base pairs. RNAbor computes the number (N), the Boltzmann partition function (Z) and the minimum free energy (MFE) and corresponding structure over the collection of all -neighbors of . This computation is done simultaneously for all m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction.
Place, publisher, year, edition, pages
2007. Vol. 23, no 16, 2054-2062 p.
Biological Sciences Computer and Information Science
IdentifiersURN: urn:nbn:se:uu:diva-96425DOI: 10.1093/bioinformatics/btm314ISI: 000249818300004OAI: oai:DiVA.org:uu-96425DiVA: diva2:170994