BioGranat-IG: BioGranat Individuals-Grouping
A tool to identify gene complexes that underlie diseases
BioGranat-IG is a bundle in BioGranat that allows the user to search a graph (i.e. a biological network) for candidate groups of genes to have a causative role in a disease. The visualisation features of BioGranat then allow the results to be displayed and explored.
BioGranat-IG is available as a plugin for BioGranat via sourceforge.
Input: BioGranat-IG is ideally suited to the analysis of exome-sequencing data. The required input consists of the graph to be analysed, together with sequencing results for multiple patients affected by the disease of interest. For each individual, a list of genes is needed where sequence variants have been found.
Output: Given this input data BioGranat-IG attempts to find the smallest connected subgraph in which all individuals have a sequence variant. If this is not possible it looks for the smallest connected subgraph containing variants for as many individuals as possible. Results can be displayed for 3D visual examination; additionally comprehensive results are produced in XML format.
Flexibility: There are several options that can be selected in BioGranat-IG giving a high level of control over the performance and the number of individuals and size of groups reported. This allows the user to interrogate the results in great detail.
User Guide
A PDF user guide is available here
Publication
Dand N, Sprengel F, Ahlers V, Schlitt T
BioGranat-IG: A network analysis tool to suggest mechanisms of genetic heterogeneity from exome sequencing data
Bioinformatics. 2013,29(6):733-741.
|
| BioGranat-IG Screenshot. BioGranat-IG is available as a plugin for BioGranat via sourceforge. |