%0 Journal Article
%T xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features
%A Shannon D Schlueter
%A Matthew D Wilkerson
%A Qunfeng Dong
%A Volker Brendel
%J Genome Biology
%D 2006
%I BioMed Central
%R 10.1186/gb-2006-7-11-r111
%X Computational infrastructure is vital for all aspects of genome research. The assembled genomic sequence of an organism provides a natural scaffold for organizing biologic data. However, researchers are easily overwhelmed if they do not have the computational tools necessary to interpret the features of these assemblies [1-4]. Although a large number of useful tools are available, they exist primarily as ad hoc collections [5-7]. The xGDB software was designed to provide a framework for genomic data storage, display and analysis, and to provide integration of existing and novel genome analysis tools. The software is portable and easily installed for either public access or as a private workbench. It comes ready to use with the following features and capabilities: detailed feature record pages; detailed views of genomic contexts; support for online community annotation; utilities for storage of feature data in relational databases; effortless integration and attachment of analysis tools; transcript view, which is a novel nucleotide resolution view of genomic contexts; compressed storage and dynamic retrieval of feature evidence alignments; attachment and organization of multiple URLs to any feature in any context; and integrated heuristic searches based on feature identifier, alias, and/or description.It is important to note that xGDB differs from and is complementary to database systems such as GMOD [8], EnsEMBL [9], and GenBank [10]. Unlike these systems, which are tasked to provide encompassing data storage, xGDB instances are applied to specific research oriented tasks, which are enabled by the browser and integrated analysis tools. Because of the varying reliability of genomic features, there is a strong need to go beyond simply plotting such features for display (as would be available in GBrowse [8], for example). Contextual analysis of genomic features often requires filtering each feature by criteria specific to an individual user's needs. Such filtering requ
%U http://genomebiology.com/2006/7/11/R111