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Two examples of frequently used methods that have problems correctly aligning proteins related by circular permutation are dynamic programming and many hidden Markov models. [34] As an alternative to these, a number of algorithms are built on top of non-linear approaches and are able to detect topology -independent similarities, or employ ...
The set X may represent a finite set of beads, and G may be a chosen group of permutations of the beads. For example, if X is a necklace of n beads in a circle, then rotational symmetry is relevant so G is the cyclic group C n, while if X is a bracelet of n beads in a circle, rotations and reflections are relevant so G is the dihedral group D n ...
There are a few equivalent ways to state this definition. A cyclic order on X is the same as a permutation that makes all of X into a single cycle, which is a special type of permutation - a circular permutation. Alternatively, a cycle with n elements is also a Z n-torsor: a set with a free transitive action by a finite cyclic group. [1]
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A cyclic permutation consisting of a single 8-cycle. There is not widespread consensus about the precise definition of a cyclic permutation. Some authors define a permutation σ of a set X to be cyclic if "successive application would take each object of the permuted set successively through the positions of all the other objects", [1] or, equivalently, if its representation in cycle notation ...
1. Carmichael's definition of circular permutation (A permutation such as ... is called a circular permutation or a cyclic permutation. [and later] A circular permutation on two letters, such as (ab), is called a transposition. [and his first theorem is] Any given permutation is a product of circular permutations no two of which have a letter ...
Given a permutation (called the text) of length and another permutation of length (called the pattern), the permutation pattern matching (PPM) problem asks whether is contained in . When both n {\displaystyle n} and k {\displaystyle k} are regarded as variables, the problem is known to be NP-complete , and the problem of counting the number of ...