Services: Genes and genomes

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets. 

Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. It provides a large variety of tree layouts, drawing and annotation features including circular tree layout, which is well-suited particularly for mid-sized trees (up to several thousand leaves). Tree displays can be exported in several graphical formats, both bitmap and vector based. Part of the Microbiome Analysis Toolbox. 

ITSoneDB is a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

Jalview is a Win/Mac/Linux/Web interactive graphical interface and command line tool for molecular sequence, alignment and 3D structure bioinformatics resource interoperability.

A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.

Species focused genome data resource for sea lice, provides a genome browser, access to high-throughput data and LIMS.

LoRDEC is a standalone software for error correcting long reads (from Pacific Biosciences, or Oxford Nanopore) with a hybrid approach. LoRDEC uses short reads to correct long reads; it combines sequencing data from both the second and third generation technologies. It can be easily integrated in any pipeline for processing deep sequencing data. LoRDEC's originality is to build a graph that summarize all short reads, and then to align the long reads against this graph to correct them. This makes LoRDEC a very efficient tool to process large datasets. It has been widely used in whole genome or transcriptome projects around the world.

A web tool for the integrative analysis of in silico miRNA target predictions, and reconstruction of post-transcriptional and mixed regulatory networks. 

(Service no longer available?) 

Freely accessible microbial genomics and metagenomics reference databases that include MarRef, MarDB, and MarCat. The MMP also includes a search engine that you can use to query all three databases at once.

Development of the software plattform for MassBank, a database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).

A tool for genome scaffolding that exploits information obtained from a set of (draft or closed) genomes to determine the correct order and orientation of the contigs.

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers thousands of publicly available gene expression data sets from ArrayExpress database.

The META-pipe pipeline for annotation and analysis of marine metagenomics samples provides insight into phylogenetic diversity and metabolic and functional potential of environmental communities.

Interactive viewer of metadynamics results.

METAGEN performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments - namely MNXref - and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

MetExplore is a free and open webserver for the analysis of omics data in the context of genome scale metabolic networks. MetExplore allows the collaborative curation of metabolic networks. In the specific case of metabolomics, it provides mining algorithms such as MetaboRank, a recommendation system for enhanced metabolic fingerprinting. Overall, Metexplore orginality relies in its ability to allow taylor made metabolic network visualisation using an open source javascript library: MetExploreViz.

MetFrag is a system for the annotation of tandem mass spectra of metabolites, performing in silico fragmentation and scoring.

Formerly called EBI Metagenomics, MGnify is an automated pipeline for the analysis and archiving of metagenomic data.

Providing a large infrastructure for the analysis and interpretation of metagenomics data

A software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference

MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.

A manually curated database of animal small non-coding RNAs

MITOchondrial genome database of metaZOAns, a resource for comparative analyses of metazoan mitochondrial genomes at the sequence and genomic levels.

A highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from NGS data. Predicts mitochondrial haplogroups.

A tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution.  It uses nearest neighbour DNA binding thermodynamics to estimate unwanted pairings between PCR samples.

The NERC Environmental Omics Facility (NEOF) will enable environmental researchers in the UK to access the full range of omics supporting technology.

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response. This resource supports COVID-19 / SARS-CoV-2 research.