Sievers Fabian, Higgins Desmond G
Conway Institute, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
Bioinformatics. 2020 Jan 1;36(1):90-95. doi: 10.1093/bioinformatics/btz552.
Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest.
We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks.
QuanTest2 is available at http://bioinf.ucd.ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script.
Supplementary data are available at Bioinformatics online.
QuanTest基准测试中的二级结构预测准确率（SSPA）可用于衡量多序列比对的准确性。如果对多个比对结果进行平均，而不是逐个比对进行，SSPA与双序列和评分密切相关。这是由于QuanTest中参考序列和非参考序列的选择不够优化。
我们为新的基准测试QuanTest2开发了一种改进的参考序列和非参考序列选择策略。在QuanTest2中，逐个比对时，SSPA和双序列和评分（SP）的相关性比在QuanTest中更好。与QuanTest相比，QuanTest2的引导树在参考序列方面更加平衡。QuanTest2的分数与其他成熟的基准测试密切相关。
QuanTest2可在http://bioinf.ucd.ie/quantest2.tar获取，包括参考序列集、非参考序列集和一个评分脚本。
补充数据可在《生物信息学》在线获取。
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