General Combinatorics of RNA Secondary Structure
نویسندگان
چکیده
منابع مشابه
Combinatorics of RNA Secondary Structures
Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as certain structural elements (sub-graphs). First order asymptotics are derived and their dependence on the logic of base pairing is computed and discussed.
متن کاملCombinatorics on Plane Trees, Motivated by RNA Secondary Structure Configurations
Motivated by the base pairing of RNA sequences, and as part of our collaboration with A. Condon and H. H. Hoos, we defined the local move operation on two unobstructed edges in a plane tree given here. We now consider the graph Gn induced by this operation on Tn, the set of plane trees with n edges. We provide a series of results showing that Gn is a connected, n-partite graph of diameter n− 1 ...
متن کاملCombinatorics of Saturated Secondary Structures of RNA
Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is -1 times the number of base pairs, saturated...
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 کاملCombinatorics of RNA Secondary Structures with Base Triples
The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to t...
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: Trends in Applied Sciences Research
سال: 2006
ISSN: 1819-3579
DOI: 10.3923/tasr.2006.273.277