Thriskos P, Zintzaras E, Germenis A
Department of Biomathematics, University of Thessaly School of Medicine, Papakyriazi 22, Larissa 41222, Greece.
Comput Methods Programs Biomed. 2007 Mar;85(3):267-72. doi: 10.1016/j.cmpb.2006.11.005. Epub 2006 Dec 28.
DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.
DHLAS（数据库HLA系统）是一个用户友好的、基于网络的信息系统，用于分析人群研究中的人类白细胞抗原（HLA）数据。DHLAS是使用JAVA和R系统开发的，它在Java虚拟机上运行，其用户界面由Servlet引擎TOMCAT提供支持，基于网络。它利用STRUTS（一种模型-视图-控制器框架），并使用几个GNU软件包来执行其多项任务。它依赖MySQL作为快速访问的数据库引擎，但也可以使用其他数据库。该系统估计指标、进行统计测试并生成HLA人群研究所需的图表：（i）哈迪-温伯格平衡（使用渐近检验和精确检验计算），（ii）遗传距离（欧几里得距离或Nei距离），（iii）使用平均加权配对组法和邻接法的系统发育树，（iv）连锁不平衡（成对和总体，包括方差估计），（v）单倍型频率（使用期望最大化算法估计）和（vi）判别分析。DHLAS的主要优点是包含了一个数据库，因此，可以将数据与综合遗传数据分析程序一起存储和处理。此外，它具有开放的架构，允许纳入其他功能和程序。
