Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 3

Genome Rearrangements Related Publications

3 On Reversal and Transposition Medians

Authors: Martin Bader

Abstract:

During the last years, the genomes of more and more species have been sequenced, providing data for phylogenetic recon- struction 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 sim- plest 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, Transpositions, me-dian, reversals

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2 Block Sorting: A New Characterization and a New Heuristic

Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

Abstract:

The Block Sorting problem is to sort a given permutation moving blocks. A block is defined as a substring of the given permutation, which is also a substring of the identity permutation. Block Sorting has been proved to be NP-Hard. Until now two different 2-Approximation algorithms have been presented for block sorting. These are the best known algorithms for Block Sorting till date. In this work we present a different characterization of Block Sorting in terms of a transposition cycle graph. Then we suggest a heuristic, which we show to exhibit a 2-approximation performance guarantee for most permutations.

Keywords: Optical Character Recognition, Genome Rearrangements, Sorting Primitives, Block Sorting, ApproximationAlgorithms

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1 Sorting Primitives and Genome Rearrangementin Bioinformatics: A Unified Perspective

Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

Abstract:

Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Genome Rearrangements, Sorting Primitives, Transpositions, Block Interchanges, Strip Exchanges

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