vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments
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- 作者：Jingming Ma (1)
Carrie Dykes (2)
Tao Wu (1)
Yangxin Huang (3)
Lisa Demeter (2)
Hulin Wu (1) - 刊名：BMC Bioinformatics
- 出版年：2010
- 出版时间：December 2010
- 年：2010
- 卷：11
- 期：1
- 全文大小：241KB
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Carrie Dykes (2)
Tao Wu (1)
Yangxin Huang (3)
Lisa Demeter (2)
Hulin Wu (1)
1. Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
2. Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
3. Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa, FL, USA - ISSN：1471-2105
文摘
Background The replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness. Results Based on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1). Conclusions Unlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/.