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首页> 外文期刊>Journal of logic and computation >Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs
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Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs

机译：基于同义块和同义包的染色体重排组合

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The reconstruction of the history of rearrangements and the reconstruction of ancestral genomes are some of the challenges of bioinformatics today. Many algorithms already exist, treating one or the other question but none treating both. These reconstructions are interdependent and we argue on the interest of treating both problems in parallel to lead to a richer and more complete output. We also argue on the importance of redefining several steps of these algorithms to improve both reconstructions: the identification of synteny blocks has to be as precise as possible, and the treatment of multiple genomes has to be based on pairwise comparisons to ensure the most detailed reconstructions. In this article, we highlight novel solutions to these points and focus on the need of explicitly treating overlapping, included, duplicated and unsigned synteny blocks. To do so, we introduce the new notion of synteny pack, which is a representation of local hypothetical intermediate ancestral genomes. We discuss a number of examples on yeast genomes to illustrate the importance of such a definition.
机译：重排历史的重建和祖先基因组的重建是当今生物信息学面临的一些挑战。已经存在许多算法，只能处理一个或另一个问题，而不能同时处理两个问题。这些重建是相互依存的，我们主张同时处理两个问题以产生更丰富和更完整的输出的利益。我们还争论了重新定义这些算法的若干步骤以改善两种重建的重要性：对同义块的识别必须尽可能精确，并且对多基因组的处理必须基于成对比较以确保最详细的重建。在本文中，我们将重点介绍针对这些问题的新颖解决方案，并将重点放在明确处理重叠，包含，重复和无符号同义块的需求上。为此，我们引入了新的“同音包”概念，它代表了局部假设的中间祖先基因组。我们讨论了酵母基因组上的许多例子，以说明这种定义的重要性。

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