Allows multiplexed putative G4 (PG4) motif mining in large number of nucleotide sequences and also enables profiling complete prokaryotic genomes. QuadBase is linked with Ensembl's genomic datasets that allows virtually any organism's latest gene models or genomic assembly to be mined for the presence of PG4 motifs. The database also allows access to search in orthologues of eukaryotic genes through Ensembl's Compara. This web server provides intuitive graphical and sequence level representations of mined PG4 motifs and the results can be accessed later or be saved in convenient formats. The web server is designed, keeping in mind the requirements of both, the experimental and computational biologists, who want deep insights in to PG4 motif occurrences in their gene sets or genome of interest.
Predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences. QGRS Mapper is a user-friendly application that provides many options for defining and studying G-quadruplexes. It performs analysis of the user provided genomic sequences, e.g. promoter and telomeric regions, as well as RNA sequences. It is also useful for predicting G-quadruplex structures in oligonucleotides. It is a user-friendly application that provides many options for defining and studying G-quadruplexes.
Provides a way to identify potential RNA G4. G4RNA screener includes several tools as G4NN, which is a novel machine learning approach trained on sequences. Its abstract representation of the sequence can be used along with developed G richness-based predictors. This serves to evaluate how a sequence relates to the known G4 of G4RNA database.
Permits exhaustive and imperfection-tolerant search for potential quadruplex-forming sequences. The pqsfinder algorithm can be divided into three logical steps: (i) identification of all possible G run quartets, (ii) score assignment and (iii) overlap resolution. It first identifies four consecutive G run sequences (G run quartet). Subsequently, it examines the potential of such G run quartet to form a stable G4 and reports a corresponding quantitative score.
An online server for prediction and bioinformatics of uni-molecular quadruplex-forming nucleotide sequences. Quadfinder enables users to discover G-quadruplex motifs in any sequence of interest. The server is designed to be user-friendly and needs minimal intervention by the user, while providing flexibility of defining the variants of the motif. The scoring of quadruplex motifs enables to prioritize motifs for further experimental studies.
Predicts thermal stability and acts as a repository for experimental data from all researchers. QuadPredict is capable of making accurate predictions of thermal stability for new sequences, having been trained on a collection of measured sequences. Computational methods have been of great use in understanding the role that G-quadruplexes may play in biology, unveiling their function in gene promoters and in regulating translation. They have also revealed that stable G-quadruplexes are generally located in nucleosome-free regions.
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garantjm Database and Web server management, Development of predictor trained by machine learning
Université de Sherbrooke