Service list

A database of structural features for three galactose metabolism enzymes (GALT, GALK, GALE).

Workflows and tools for analysis of microscopy image data and cellular phenotyping using Galaxy. Provision of expertise and support of projects requiring automatic image analysis.

Collection of tutorials developed and maintained by the worldwide Galaxy community.

Galaxy server dedicated towards public health applications: tools, pipelines and databases for using WGS in routine pathogen typing and characterization

An optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.

Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses. All code is open-source and freely available in the GEAR software repositories, including the code for the web server front-end applications and the backend genomics analysis software. Among other command-line applications, the backend code includes Tracy.

Prokaryote genome annotation system, modular, flexible and extensible.

Eukaryotic genome annotation system, modular, flexible and extensible.

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

GenExVis (Gene Expression Visualizer) is a desktop application for exploring and visualizing differential gene expression data. 

GenomeCRISPR is a database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions.

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).

The GenomeRNAi database makes available RNAi phenotype data extracted from the literature, or submitted by data producers directly, for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity.

A comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

GeoMine enables textual, numerical and 3D searching with full chemical awareness in binding sites of the entire PDB dataset. 

A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.
Using its user-friendly graphical interface, users can specify a signed regulatory graph, define boolean or multivalued logical functions, and then simulate and analyse its qualitative dynamical behaviour.

User interface to data from high-throughput sequencing studies of fungal communities across terrestrial biomes. Includes sequencing data, sample locations, sample metadata.

Glyco@Expasy centralizes web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy is that it should be {glycoscientist AND protein scientist}–friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. Glyco@Expasy was designed with glycoscientists to meet the growing needs of the community for glycoinformatics.

GlyConnect is a platform integrating several sources of information to characterise the molecular actors of glycosylation, mainly glycoproteins and N- and O-linked glycans. The purpose of GlyConnect is to bring out in a single resource the relationships between glycans, the proteins that carry them, the enzymes that synthesise or degrade them and the proteins that bind them.

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

The UniProt  GO annotation program (GOA) aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).

Detection of distinct Galpha families, Gbeta and Ggamma subunits of heterotrimeric G-proteins using profile Hidden Markov Models (pHMMs).

GraphWeb is a public web server for graph-based analysis of biological networks.

gtrellis is an R package which facilitates genome-level trellis layout, for enhancing visualisation and graphical layout

The GTPB runs face-to-face Bioinformatics Training Courses regularly at the Instituto Gulbenkian de Ciência.

The NHGRI-EBI GWAS Catalog is a quality-controlled, manually curated, literature-derived collection of all published genome-wide association studies.
 

Providing a centralized compilation of summary level findings from genetic association studies, both large and small

HAMAP is a system for the classification and functional annotation of protein sequences. It consists of a collection of expert curated family profiles for protein classification and associated rules for protein annotation.