Data analysis and processing: creation of new bioinformatics tools in RD-Connect

5 May 2015


The rapidly increasing number of new omics projects is resulting in the generation of an unprecedented volume of data. These data are useless unless we can harness the power of sophisticated computer software – bioinformatics tools – to analyse, filter and interpret them. In addition, linking the omics data with phenotypic data accurately annotated using standardized codes and ontologies is essential for interpretation of the data. Within RD-Connect a dedicated work-package, led by Christophe Béroud at Aix-Marseille University, focuses on the development of bioinformatic tools. The development of such tools will aid data interpretation, data mining and knowledge discovery and help facilitate the discovery of new genes, pathways and therapeutic targets. This work package has already produced several systems that are now available for the scientific community. Partners in the collaborating projects NeurOmics and EURenOmics are also developing software tools and systems addressing aspects of relevance to their work.

The following bioinformatics tools and other related resources are being developed within or will be made available through the NeurOmics, EURenOmics and RD-Connect consortia. Further information is available on the RD-Connect website by clicking on the relevant tool name below.

Alamut Batch: is an efficient high-throughput human variant annotation engine for studies ranging from gene panels to exome NGS analyses.

Alamut Focusis an interactive variant filtration application for NGS analysis. Alamut Focus is fully compatible with Alamut Batch and Alamut Visual.

Alamut Visual: is an intuitive graphical gene browser visualizing well-curated and clinically oriented data gathered from reliable public databases.

Alamut Functional Annotations (ALFA): is a gene regulation prediction software tool designed to identify genomic variations located in non-coding DNA that may be involved in gene regulation processes.

COEUSis a Semantic Web Application Framework that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems.

Diseasecard: is a mature collaborative portal focused on the integration and dissemination of genetic and medical information regarding rare genetic diseases.

Bio Relations and Intelligence Network (BRAIN): enables users to create mind maps that visualize the relations between biological concepts, such as genes and diseases. This makes it possible to access the data sources all at once, circumventing the need to visit them individually.

GeneGridis a tool for identifying relevant variants from exome or whole genome sequencing that is being developed by Genomatix, a partner in the EURenOmics consortium. The software can be used for case/control scenarios or trio analyses. It can be applied for cancer studies as well as rare disease research.

Human Splicing Finder (HSF)combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites and the branch point and auxiliary sequences known to either enhance (Exonic Splicing Enhancers) or repress splicing (Exonic Splicing Silencers).

PhenomeCentral: is a collaborative effort which aims to address the common challenge of exome and genome sequencing in both the research and clinical settings. Through a remote matching API for finding genotypically and phenotypically similar patients, Phenomecentral enables clinicians and scientists to share information about patients with similar phenotypes and genotypes.

PhenoTipsis a user-friendly open source software tool that enables clinicians to collect and analyze phenotypic information for patients with genetic disorders using the Human Phenotype Ontology.

The Rare Diseases Registry Framework (RDRF): has many desirable features which include its ability to create multiple registries within the same framework, patients are defined once but can belong to more than one registry, and the ability for curators to create data elements dynamically well after the registry has been defined, enabling the registry to adapt to the evolving requirements of data capture.

UMD-Predictoris a new computational combinatorial system that efficiently annotates cDNA substitutions of all human transcripts for their potential pathogenicity.

VarAFT (Variant Analysis and Filtration Tool)permits end-users to annotate, analyze and highlight causative mutations based on a large panel of filtration options.

Yabi: is an online research environment that provides rare disease researchers with an intuitive, easy to use web-based environment for creating, running and managing bioinformatics analysis workflows.