StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.
StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.
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DOI：
10.3389/fbinf.2021.704157
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Borodovsky, Mark
中科院分区：
文献类型：
--
作者：
Gemayel, Karl;Lomsadze, Alexandre;Borodovsky, Mark
关键词：
原核基因组从头开始基因预测的最先进算法被证明是足够准确的。一对算法会就基因 3' 末端的预测达成一致。尽管如此，基因起始点的预测与基因组中 15-25% 的基因不匹配。这种差异是一个严重的问题，由于缺乏经过实验验证的足够大的基因组而难以解决。我们引入了 StartLink，它根据同源核苷酸序列的多重比对揭示的保守模式推断基因起始点。我们还引入了 StartLink+，结合了从头开始和基于对齐的方法。 StartLink 预测给定基因起始的能力受到数据库中同源物可用性的限制。我们观察到 StartLink 平均对每个基因组 85% 的基因进行了预测。对于经过实验验证的起始基因组，StartLink+ 的准确度为 98-99%。与数据库注释相比，我们观察到，平均而言，富含 AT 的基因组中约 5% 的基因和富含 GC 的基因组中 10-15% 的基因的注释基因开始偏离 StartLink+ 预测。 StartLink+ 的使用有可能显着改善基因组数据库中的基因起始注释。
State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on predictions of gene 3′ends. Nonetheless, predictions of gene starts would not match for 15–25% of genes in a genome. This discrepancy is a serious issue that is difficult to be resolved due to the absence of sufficiently large sets of genes with experimentally verified starts. We have introduced StartLink that infers gene starts from conservation patterns revealed by multiple alignments of homologous nucleotide sequences. We also have introduced StartLink+ combining both ab initio and alignment-based methods. The ability of StartLink to predict the start of a given gene is restricted by the availability of homologs in a database. We observed that StartLink made predictions for 85% of genes per genome on average. The StartLink+ accuracy was shown to be 98–99% on the sets of genes with experimentally verified starts. In comparison with database annotations, we observed that the annotated gene starts deviated from the StartLink+ predictions for ∼5% of genes in AT-rich genomes and for 10–15% of genes in GC-rich genomes on average. The use of StartLink+ has a potential to significantly improve gene start annotation in genomic databases.
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