作为基因和其转录本的基本单位，核苷酸对基因功能和进化、以及表型和疾病产生巨大影响。为了确定一个特定基因的关键核苷酸，定量测量每个碱基对基因的重要性非常关键。然而，目前仍没有基于序列的方法来实现这一目标。在本研究中，我们提出了一种基于人类mRNA和长非编码RNA（lncRNA）序列信息计算单个碱基重要性的算法——碱基重要性计算器（BIC）。随后，我们通过应用BIC于三个不同任务来验证其效力。首先，我们揭示了BIC能够通过单核苷酸变异有效评估基因和单个碱基的致病性。此外，BIC在癌症基因组图谱的体细胞突变中的得分能够预测某些癌症的预后。最后，我们显示了BIC还能够准确预测新型冠状病毒传播性。以上结果表明，BIC是评估人类mRNA和lncRNA单个碱基重要性的有用工具。 © 2023年 作者。牛津大学出版社所有，保留所有权利。如需获得权限，请发送电子邮件至：journals.permissions@oup.com。

As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on the gene function and evolution, and thus on phenotypes and diseases. In order to identify the key nucleotides of one specific gene, it is quite crucial to quantitatively measure the importance of each base on the gene. However, there are still no sequence-based methods of doing that. Here, we proposed Base Importance Calculator (BIC), an algorithm to calculate the importance score of each single base based on sequence information of human mRNAs and long noncoding RNAs (lncRNAs). We then confirmed its power by applying BIC to three different tasks. Firstly, we revealed that BIC can effectively evaluate the pathogenicity of both genes and single bases through single nucleotide variations. Moreover, the BIC score in The Cancer Genome Atlas somatic mutations is able to predict the prognosis of some cancers. Finally, we show that BIC can also precisely predict the transmissibility of SARS-CoV-2. The above results indicate that BIC is a useful tool for evaluating the single base importance of human mRNAs and lncRNAs.© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.