首页> 外文会议>Algorithms in bioinformatics >Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes
【24h】

Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes

机译:哺乳动物和植物基因组中的解码同义块和大规模重复。

获取原文
获取原文并翻译 | 示例

摘要

The existing synteny block reconstruction algorithms use anchors (e.g., orthologous genes) shared over all genomes to construct the synteny blocks for multiple genomes. This approach, while efficient for a few genomes, cannot be scaled to address the need to construct synteny blocks in many mammalian genomes that are currently being sequenced. The problem is that the number of anchors shared among all genomes quickly decreases with the increase in the number of genomes. Another problem is that many genomes (plant genomes in particular) had extensive duplications, which makes decoding of genomic architecture and rearrangement analysis in plants difficult. The existing synteny block generation algorithms in plants do not address the issue of generating non-overlapping synteny blocks suitable for analyzing rearrangements and evolution history of duplications. We present a new algorithm based on the A-Bruijn graph framework that overcomes these difficulties and provides a unified approach to synteny block reconstruction for multiple genomes, and for genomes with large duplications.
机译:现有的同义块重建算法使用在所有基因组上共享的锚(例如直系同源基因)来构建多个基因组的同义块。这种方法虽然对一些基因组有效,但不能扩展到解决目前正在测序的许多哺乳动物基因组中构建同义模块的需求。问题在于,随着基因组数量的增加,所有基因组之间共享的锚点数量迅速减少。另一个问题是许多基因组(尤其是植物基因组)具有大量重复,这使得植物中基因组结构的解码和重排分析变得困难。植物中现有的同步块生成算法没有解决生成适用于分析重复的重排和进化历史的不重叠的同步块的问题。我们提出了一种基于A-Bruijn图框架的新算法,该算法克服了这些困难,并为多个基因组以及具有大重复量的基因组提供了统一的共生块重建方法。

著录项

  • 来源
    《Algorithms in bioinformatics》|2009年|220-232|共13页
  • 会议地点 Philadelphia PA(US);Philadelphia PA(US)
  • 作者单位

    Department of Computer Science and Engineering University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093;

    Department of Computer Science and Engineering University of South Carolina, 315 Main St., Columbia, SC 29208;

    Department of Mathematics University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093;

    Department of Computer Science and Engineering University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093;

  • 会议组织
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物工程学(生物技术);
  • 关键词

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱:kefu@zhangqiaokeyan.com

京公网安备:11010802029741号 ICP备案号:京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有
  • 客服微信

  • 服务号