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

Authors:
P. Thriskos;E. Zintzaras;A. Germenis
Affiliations:
Department of Biomathematics, University of Thessaly School of Medicine, Papakyriazi 22, Larissa 41222, Greece;Department of Biomathematics, University of Thessaly School of Medicine, Papakyriazi 22, Larissa 41222, Greece;Department of Immunology and Histocompatibility, University of Thessaly School of Medicine, Larissa, Greece
Venue:
Computer Methods and Programs in Biomedicine
Year:
2007

Citing 3
Cited 4

Haploview: analysis and visualization of LD and haplotype maps

Bioinformatics
A tree-based decision rule for identifying profile groups of cases without predefined classes: application in diffuse large B-cell lymphomas

Computers in Biology and Medicine
Non-parametric classification of protein secondary structures

Computers in Biology and Medicine

A SOA statistical engine for biomedical data

Computer Methods and Programs in Biomedicine
A Humanized Mandarin e-Learning System Based on Pervasive Computing

Edutainment '08 Proceedings of the 3rd international conference on Technologies for E-Learning and Digital Entertainment
Web-based Multi-center Data Management System for Clinical Neuroscience Research

Journal of Medical Systems
WebBio, a Web-Based Management and Analysis System for Patient Data of Biological Products in Hospital

Journal of Medical Systems

Quantified Score

Hi-index	0.00

Visualization

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.