DHLAS: A web-based information system for statistical genetic analysis of HLA population data

Abstract 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 b...

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Bibliographic Details
Published in:Computer methods and programs in biomedicine 2007-03, Vol.85 (3), p.267-272
Main Authors: Thriskos, P, Zintzaras, E, Germenis, A
Format: Article
Language:English
Subjects:
Bioinformatics
Databases, Genetic
Greece
HLA
HLA Antigens - genetics
Humans
Information system
Internal Medicine
Internet
Other
Statistical genetics
User-Computer Interface
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Summary:Abstract 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.
ISSN:0169-2607
1872-7565
DOI:10.1016/j.cmpb.2006.11.005