- Cocitations is an online service on a database that indexes sentences from PubMed references that mention at least two gene names. The user queries the database by specifying a gene name of a given species (only Bacillus subtilis is currently supported), and select the second gene by browsing through the list of all cocited genes. The corresponding references or sentences are then displayed, and the occurrences of gene names are highlighted.
- CompaGB is an online framework providing facilities to evaluate and compare Genome Browsers functionalities as tables or radar graphs. It also offers the possibility of weighting the criteria to fit a user specific context. This project is open and free, we invite anyone in the community to perform new evaluations as well as concurrent evaluations of already evaluated softwares. The list of criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features.
- DOMIRE (DOMain Identification from REcurrence) is a server using VAST (Vector Alignment Search Tool, protein 3D structure comparison , free download here) to define the domain boundaries in proteins from their 3 D structures (Samson, F., Shrager, R., Tai, C.-H., Sam, V., Lee, B.-K., Munson, P., Gibrat, J.-F. and Garnier, J. (2012). Domire: a web server for identifying structural domains and their neighbors in proteins. Bioinformatics. 28 (7) 1040-1041. [ DOI ]). It provides also a list of structural neighbours.
- Insyght, based on a genomic database, proposes a new way to explore the landscape of conserved and idiosyncratic genomic regions across multiple genomes and their rearrangements throughout evolution. Its unique display consists of a symbolic representation tightly integrated with a proportional view. The symbols highlight a region of interest and provide legibility while the proportional view simultaneously allows grasping genomic locations and complex rearrangements scattered across the genomes and occurring at different scales. A second type of display is dedicated to the analysis of the presence / absence / multiple copies of a given set of homologs. A functionality based on filters has been implemented to facilitate the retrieval of genes of interest and allow the formulation of relevant biological questions, such as finding niche-specific or core genome genes that match a few particular functions or biological processes. Scope of analysis: genome-wide inference of gene function, detection of evolutionary events, phylogenetic profiling and investigation of the core genome or niche-specific genes.
- FROST (Fold Recognition Oriented Search Tool) searches a compatible fold for a given protein amino acid sequence (Marin, J. Pothier, K. Zimmermann and J.-F. Gibrat. FROST: a filter-based fold recognition method. Proteins, 2002 Dec 1; 49(4): 493-509 [PubMed])
- GPCRautomodel : G-protein-coupled receptors (GPCRs) are key components of several cellular response mechanisms to environmental signals. GPCRautomodel allows users to carry out high-throughput modeling of olfactory receptor proteins from their amino acid sequence and docking of odorant molecules on the model 3D structures (Launay et al., PEDS 2012).