Abstract: The median problem is significantly applied to derive
the most reasonable rearrangement phylogenetic tree for many
species. More specifically, the problem is concerned with finding
a permutation that minimizes the sum of distances between itself
and a set of three signed permutations. Genomes with equal number
of genes but different order can be represented as permutations.
In this paper, an algorithm, namely BeamGA median, is proposed
that combines a heuristic search approach (local beam) as an
initialization step to generate a number of solutions, and then a
Genetic Algorithm (GA) is applied in order to refine the solutions,
aiming to achieve a better median with the smallest possible reversal
distance from the three original permutations. In this approach,
any genome rearrangement distance can be applied. In this paper,
we use the reversal distance. To the best of our knowledge, the
proposed approach was not applied before for solving the median
problem. Our approach considers true biological evolution scenario
by applying the concept of common intervals during the GA
optimization process. This allows us to imitate a true biological
behavior and enhance genetic approach time convergence. We were
able to handle permutations with a large number of genes, within
an acceptable time performance and with same or better accuracy as
compared to existing algorithms.
Abstract: The biological function of an RNA molecule depends
on its structure. The objective of the alignment is finding the
homology between two or more RNA secondary structures. Knowing
the common functionalities between two RNA structures allows
a better understanding and a discovery of other relationships
between them. Besides, identifying non-coding RNAs -that is not
translated into a protein- is a popular application in which RNA
structural alignment is the first step A few methods for RNA
structure-to-structure alignment have been developed. Most of these
methods are partial structure-to-structure, sequence-to-structure, or
structure-to-sequence alignment. Less attention is given in the
literature to the use of efficient RNA structure representation and the
structure-to-structure alignment methods are lacking. In this paper,
we introduce an O(N2) Component-based Pairwise RNA Structure
Alignment (CompPSA) algorithm, where structures are given as
a component-based representation and where N is the maximum
number of components in the two structures. The proposed algorithm
compares the two RNA secondary structures based on their weighted
component features rather than on their base-pair details. Extensive
experiments are conducted illustrating the efficiency of the CompPSA
algorithm when compared to other approaches and on different real
and simulated datasets. The CompPSA algorithm shows an accurate
similarity measure between components. The algorithm gives the
flexibility for the user to align the two RNA structures based on
their weighted features (position, full length, and/or stem length).
Moreover, the algorithm proves scalability and efficiency in time and
memory performance.