GenoLink：一种基因图形的查询和浏览系统分析基因和蛋白质表达

生物谷

Genolink是Genostar公司刚刚开发出来一种基于图形和浏览界面的基因和蛋白质表达分析系统，通过图形形式显示大规模基因组和蛋白质组学数据，同时这一软件还有强大的查询分析功能。

GenoLink's strength lies in the fact that it can explicitly represent and manipulate relationships between biological entities. These include similarities between genes, functional families, existence of syntenies and physical interaction between proteins.
GenoLink allows the user to build advanced queries based on these relationships, and to browse the results through a powerful and intuitive interface.

		GenoLink brings insight into new relationships by progressively browsing through the different types of link that relate a given entity, such as a gene or a protein, to another relevant entity. Such correlations may suggest, for instance the function of an orphan gene.

GenoLink thus extends the annotation process initiated by GenoAnnot towards the characterization of the functions of gene products.

Background

A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs.

Results

GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces.

Conclusions

GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also http://www.genostar.org.

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