On Reversal and Transposition Medians
نویسنده
چکیده
During the last years, the genomes of more and more species have been sequenced, providing data for phylogenetic reconstruction based on genome rearrangement measures. A main task in all phylogenetic reconstruction algorithms is to solve the median of three problem. Although this problem is NP-hard even for the simplest distance measures, there are exact algorithms for the breakpoint median and the reversal median that are fast enough for practical use. In this paper, this approach is extended to the transposition median as well as to the weighted reversal and transposition median. Although there is no exact polynomial algorithm known even for the pairwise distances, we will show that it is in most cases possible to solve these problems exactly within reasonable time by using a branch and bound algorithm. Keywords—Comparative genomics, genome rearrangements, median, reversals, transpositions.
منابع مشابه
Median clouds and a fast transposition median solver
The median problem seeks a permutation whose total distance to a given set of permutations (the base set) is minimal. This is an important problem in comparative genomics and has been studied for several distance measures such as reversals. The transposition distance is less relevant biologically, but it has been shown that it behaves similarly to the most important biological distances, and ca...
متن کاملReversal and Transposition Distance of Linear Chromosomes
In recent years we are seeing increasing interest in research on mutational events acting on large portions of the chromosomes. Among these events, a reversal acts on a fragment of a chromosome reversing the order and orientation of the genes, and a transposition moves fragments from one region to another within a chromosome. In this article we analyze genomes evolving by reversals and transpos...
متن کاملA Lower Bound on the Reversal and Transposition Diameter
One possible model to study genome evolution is to represent genomes as permutations of genes and compute distances based on the minimum number of certain operations (rearrangements) needed to transform one permutation into another. Under this model, the shorter the distance, the closer the genomes are. Two operations that have been extensively studied are the reversal and the transposition. A ...
متن کاملThe transposition median problem is NP-complete
During the last years, the genomes of more and more species have been sequenced, providing data for phylogenetic reconstruction based on genome rearrangement measures, where the most important distance measures are the reversal distance and the transposition distance. The two main tasks in all phylogenetic reconstruction algorithms is to calculate pairwise distances and to solve the median of t...
متن کاملUsing median sets for inferring phylogenetic trees
MOTIVATION Algorithms for phylogenetic tree reconstruction based on gene order data typically repeatedly solve instances of the reversal median problem (RMP) which is to find for three given gene orders a fourth gene order (called median) with a minimal sum of reversal distances. All existing algorithms of this type consider only one median for each RMP instance even when a large number of medi...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2009