United States Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
BMC Bioinformatics. 2012 Jun 22;13:143. doi: 10.1186/1471-2105-13-143.
The concept of orthology is key to decoding evolutionary relationships among genes across different species using comparative genomics. QuartetS is a recently reported algorithm for large-scale orthology detection. Based on the well-established evolutionary principle that gene duplication events discriminate paralogous from orthologous genes, QuartetS has been shown to improve orthology detection accuracy while maintaining computational efficiency.
QuartetS-DB is a new orthology database constructed using the QuartetS algorithm. The database provides orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic), covering more than seven million proteins and four million pairwise orthologs. It is a major source of orthologous groups, containing more than 300,000 groups of orthologous proteins and 236,000 corresponding gene trees. The database also provides over 500,000 groups of inparalogs. In addition to its size, a distinguishing feature of QuartetS-DB is the ability to allow users to select a cutoff value that modulates the balance between prediction accuracy and coverage of the retrieved pairwise orthologs. The database is accessible at https://applications.bioanalysis.org/quartetsdb.
QuartetS-DB is one of the largest orthology resources available to date. Because its orthology predictions are underpinned by evolutionary evidence obtained from sequenced genomes, we expect its accuracy to continue to increase in future releases as the genomes of additional species are sequenced.
使用比较基因组学来解码不同物种之间基因的进化关系，同源性的概念是关键。QuartetS 是一种最近报道的大规模同源性检测算法。基于基因复制事件区分同源和旁系同源基因的既定进化原则，QuartetS 被证明可以提高同源性检测的准确性，同时保持计算效率。
QuartetS-DB 是一个使用 QuartetS 算法构建的新的同源性数据库。该数据库提供了 1621 个完整基因组（1365 个细菌、92 个古细菌和 164 个真核生物）之间的同源性预测，涵盖了超过 700 万个蛋白质和 400 万个成对的同源物。它是同源物组的主要来源，包含了 30 多万个同源蛋白组和 236000 个相应的基因树。该数据库还提供了超过 50 万个同系物组。除了其规模之外，QuartetS-DB 的一个显著特点是能够让用户选择一个截止值，该值调节预测准确性和检索到的成对同源物的覆盖范围之间的平衡。该数据库可在 https://applications.bioanalysis.org/quartetsdb 访问。
QuartetS-DB 是迄今为止可用的最大的同源性资源之一。由于其同源性预测是基于从测序基因组中获得的进化证据，我们预计随着更多物种的基因组被测序，其准确性将在未来的版本中继续提高。
