Strategies for measuring evolutionary conservation of RNA secondary structures

Measuring Evolutionary Isolation for Conservation

Conservation planning needs to account for limited resources when choosing those species on which to focus attention and resources. Currently, funding is biased to small sections of the tree of life, such as raptors and carnivores. One new approach for increasing the diversity of species under consideration considers how many close relatives a species has in its evolutionary tree. At least elev...

An evolutionary basis for conservation strategies.

RNA Secondary Structures

The central dogma of molecular biology states that the flow of information is from DNA, through RNA, to proteins. What this means is that DNA is the storage medium of genomic information, while proteins are the molecules with functional and structural rôles. In this view, RNA is mostly considered a ‘supporting actor’, being the medium used for transporting information from storage to where it i...

Statistics of RNA secondary structures.

A statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops, joints, and free ends. Statistical properties of ...

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.