Computer Technologies Laboratory, School of Translational Information Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg 197101, St. Petersburg, Russian Federation.
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
Gigascience. 2020 Jun 1;9(6). doi: 10.1093/gigascience/giaa047.
Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production.
halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred-way, reference-free vertebrate alignments built with the Cactus system.
halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.
大规模测序项目提供了高质量的全基因组数据，可用于重建破坏保守同线性块的染色体交换和重排。基于全基因组、无参考的比对，可以获得跨物种同源性的最高分辨率。以二进制格式存储的全基因组序列的非常大的多重比对需要一种准确高效的计算方法来生成同线性块。
halSynteny 可以为比对中的任何一对基因组高效处理成对比对块。该工具是 HAL 比较基因组学套件的一部分，旨在为使用 Cactus 系统构建的具有数百种无参考脊椎动物比对的同线性块。
halSynteny 能够在多个全基因组比对中准确快速地识别同线性。该方法在 C++11 中实现，作为 halTools 软件的一个组件，并根据 MIT 许可证发布。该软件包可在 https://github.com/ComparativeGenomicsToolkit/hal/ 获得。
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