病毒病原体资源（ViPR）中的丙型肝炎病毒数据库及生物信息学分析工具。

Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR).

作者信息

Zhang Yun, Zmasek Christian, Sun Guangyu, Larsen Christopher N, Scheuermann Richard H

机构信息

J. Craig Venter Institute, La Jolla, CA, USA.

Vecna Technologies, Greenbelt, MD, USA.

出版信息

Methods Mol Biol. 2019;1911:47-69. doi: 10.1007/978-1-4939-8976-8_3.

DOI:10.1007/978-1-4939-8976-8_3

PMID:30593617

Abstract

The Virus Pathogen Resource (ViPR; www.viprbrc.org ) is a US National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center providing bioinformatics support for major human viral pathogens. The hepatitis C virus (HCV) portal of ViPR facilitates basic research and development of diagnostics and therapeutics for HCV, by providing a comprehensive collection of HCV-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, and personal Workbench spaces for data storage and sharing. This chapter introduces the data and functionality provided by the ViPR HCV portal. It describes example workflows for (1) searching HCV genome and protein sequences, (2) conducting phylogenetic analysis, and (3) analyzing sequence variations using pattern search for amino acid substitutions in proteins, single nucleotide variation calculation, metadata-driven comparison, and sequence feature variant type analysis. All data and tools are freely available via the ViPR HCV portal at https://www.viprbrc.org/brc/home.spg?decorator=flavi_hcv .

摘要

病毒病原体资源库（ViPR；www.viprbrc.org）是美国国立过敏与传染病研究所（NIAID）资助的生物信息学资源中心，为主要的人类病毒病原体提供生物信息学支持。ViPR的丙型肝炎病毒（HCV）门户通过提供从各种来源整合的HCV相关数据的全面集合、用于数据挖掘和假设生成的不断增加的分析和可视化工具套件，以及用于数据存储和共享的个人工作台空间，促进了HCV诊断和治疗的基础研究与开发。本章介绍了ViPR HCV门户提供的数据和功能。它描述了以下示例工作流程：（1）搜索HCV基因组和蛋白质序列，（2）进行系统发育分析，以及（3）使用蛋白质中氨基酸取代模式搜索、单核苷酸变异计算、元数据驱动比较和序列特征变异类型分析来分析序列变异。所有数据和工具均可通过ViPR HCV门户（https://www.viprbrc.org/brc/home.spg?decorator=flavi_hcv）免费获取。