Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Bioinformatics. 2019 Jan 1;35(1):149-151. doi: 10.1093/bioinformatics/bty631.
Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ.
Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets.
SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid.
Supplementary data are available at Bioinformatics online.
同源基因推断是许多基于基因组的研究的共同基础，是注释新基因组、寻找生物技术应用的目标基因和揭示生命进化历史的前提。尽管随着测序基因组数量的不断增加，其重要性不断提高，但现有的工具计算要求高，难以使用。
在这里，我们提出了 SonicParanoid，它比成熟的工具更快，但准确性相当，具有平衡的精度-召回权衡。此外，SonicParanoid 大大减轻了那些需要构建和维护自己基因组数据集的人进行同源基因推断的困难。
SonicParanoid 可在 Python 包索引和 BitBucket 上使用 GNU GPLv3 许可证获得。文档可在 http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid 上获得。
补充数据可在生物信息学在线获得。
