vFitness: a web-based computing tool for improving estimation of <it>in vitro </it>HIV-1 fitness experiments

• Main Authors: Demeter Lisa, Huang Yangxin, Wu Tao, Dykes Carrie, Ma Jingming, Wu Hulin
• Format: Article
• Language: English
• Published: BMC 2010-05-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/11/261

<p>Abstract</p> <p>Background</p> <p>The replication rate (or fitness) between viral variants has been investigated <it>in vivo </it>and <it>in vitro </it>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.</p> <p>Results</p> <p>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).</p> <p>Conclusions</p> <p>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 <url>http://bis.urmc.rochester.edu/vFitness/</url>.</p>