RNA Locally Optimal Secondary Structures
نویسندگان
چکیده
منابع مشابه
RNA Locally Optimal Secondary Structures
RNA locally optimal secondary structures provide a concise and exhaustive description of all possible secondary structures of a given RNA sequence, and hence a very good representation of the RNA folding space. In this paper, we present an efficient algorithm that computes all locally optimal secondary structures for any folding model that takes into account the stability of helical regions. Th...
متن کاملCombinatorics of locally optimal RNA secondary structures.
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair con...
متن کاملRNALOSS: a web server for RNA locally optimal secondary structures
RNAomics, analogous to proteomics, concerns aspects of the secondary and tertiary structure, folding pathway, kinetics, comparison, function and regulation of all RNA in a living organism. Given recently discovered roles played by micro RNA, small interfering RNA, riboswitches, ribozymes, etc., it is important to gain insight into the folding process of RNA sequences. We describe the web server...
متن کاملFinding stable local optimal RNA secondary structures
MOTIVATION Many RNAs, such as riboswitches, can fold into multiple alternate structures and perform different biological functions. These biologically functional structures usually have low free energies in their local energy landscapes and are very stable such that they cannot easily jump out of the current states and fold into other stable conformations. The conformational space of feasible R...
متن کاملApproximately Counting Locally-Optimal Structures
In general, constructing a locally-optimal structure is a little harder than constructing an arbitrary structure, but significantly easier than constructing a globally-optimal structure. A similar situation arises in listing. In counting, most problems are #P-complete, but in approximate counting we observe an interesting reversal of the pattern. Assuming that #BIS is not equivalent to #SAT und...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2012
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2010.0178