Zhou Zhan, Wu Jingcheng, Ren Jianan, Chen Wenfan, Zhao Wenyi, Gu Xun, Chi Ying, He Qiaojun, Yang Bo, Wu Jian, Chen Shuqing
Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China.
Comput Struct Biotechnol J. 2021 Aug 12;19:4510-4516. doi: 10.1016/j.csbj.2021.08.016. eCollection 2021.
TSNAD is a one-stop software solution for predicting neoantigens from the whole genome/exome sequencing data of tumor-normal pairs. Here we present TSNAD v2.0 which provides several new features such as the function of RNA-Seq analysis including gene expression and gene fusion analysis, the support of different versions of the reference genome. Most importantly, we replace the NetMHCpan with DeepHLApan we developed previously, which considers both the binding between peptide and major histocompatibility complex (MHC) and the immunogenicity of the presented peptide-MHC complex (pMHC). TSNAD v2.0 achieves good performamce on a standard dataset. For better usage, we provide the Docker version and the web service of TSNAD v2.0. The source code of TSNAD v2.0 is freely available at https://github.com/jiujiezz/tsnad. And the web service of TSNAD v2.0 is available at http://biopharm.zju.edu.cn/tsnad/.
TSNAD是一种一站式软件解决方案，用于从肿瘤-正常组织配对的全基因组/外显子组测序数据中预测新抗原。在此，我们展示TSNAD v2.0，它提供了几个新功能，如RNA测序分析功能，包括基因表达和基因融合分析，支持不同版本的参考基因组。最重要的是，我们用我们之前开发的DeepHLApan取代了NetMHCpan，DeepHLApan同时考虑了肽与主要组织相容性复合体（MHC）之间的结合以及所呈现的肽-MHC复合体（pMHC）的免疫原性。TSNAD v2.0在一个标准数据集上取得了良好的性能。为了更好地使用，我们提供了TSNAD v2.0的Docker版本和网络服务。TSNAD v2.0的源代码可在https://github.com/jiujiezz/tsnad上免费获取。TSNAD v2.0的网络服务可在http://biopharm.zju.edu.cn/tsnad/上获取。
Zotero 插件
