TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection

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...

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Detalles Bibliográficos
Autores principales: Zhou, Zhan, Wu, Jingcheng, Ren, Jianan, Chen, Wenfan, Zhao, Wenyi, Gu, Xun, Chi, Ying, He, Qiaojun, Yang, Bo, Wu, Jian, Chen, Shuqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2021
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8385119/
https://www.ncbi.nlm.nih.gov/pubmed/34471496
http://dx.doi.org/10.1016/j.csbj.2021.08.016
Descripción
Sumario: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/.

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