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TSNAD v2.0: a one-stop software solution for tumor-specific neoantigen detection
Computational and Structural Biotechnology Journal ( IF 6 ) Pub Date : 2021-08-12 , DOI: 10.1016/j.csbj.2021.08.016
Zhan Zhou 1, 2 , Jingcheng Wu 1, 3 , Jianan Ren 1 , Wenfan Chen 1, 4 , Wenyi Zhao 1, 3 , Xun Gu 5 , Ying Chi 6 , Qiaojun He 1, 2 , Bo Yang 1, 2 , Jian Wu 2, 3, 7 , Shuqing Chen 1
Affiliation  

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/.



中文翻译:

TSNAD v2.0:肿瘤特异性新抗原检测一站式软件解决方案

TSNAD 是一种一站式软件解决方案,用于从肿瘤-正常对的全基因组/外显子组测序数据中预测新抗原。在这里,我们展示了 TSNAD v2.0,它提供了几个新功能,例如 RNA-Seq 分析的功能,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 替换了 NetMHCpan,它考虑了肽和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 在标准数据集上取得了良好的性能。为了更好的使用,我们提供了 Docker 版本和 TSNAD v2.0 的 web 服务。TSNAD v2.0 的源代码可在https://github.com/jiujiezz/tsnad免费获得. TSNAD v2.0 的网络服务可在http://biopharm.zju.edu.cn/tsnad/ 获得

更新日期:2021-08-12
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