Services: Genes And Genomes

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.

The mOTUs tool uses phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) to profile microorganisms at species-level resolution when using metagenomic data as input. Since the MGs represent housekeeping genes, mOTUs can also be used to profile transcriptionally active community members when using metatranscriptomic data as input. Furthermore, MG-based SNV profiling provides an efficient alternative to using whole genome sequences to compare microbial strain populations.

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.

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.

OMA identifies orthologs among 2000 genomes from all domains of life. Other distinctive characteristics are the high quality of its inferences, the feature-rich web interface, and frequent update schedule of two releases per year. 

Orphadata provides the scientific community with comprehensive, quality data sets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.

Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases.

OrthoDB is a comprehensive catalog of evolutionary and functional annotations of orthologs, covering over 22 million genes from over 5000 species of animals, fungi, plants, archaea, bacteria, and viruses. 

PanDrugs is a method to prioritize anticancer drug treatments according to individual genomic data. PanDrugs current version integrates data from 24 primary sources and supports 56297 drug-target associations obtained from 4804 genes and 9092 unique compounds

ParameciumDB is a community model organism database for the ciliate Paramecium. The web site gives access to genomes of many Paramecium species and their annotations. ParameciumDB also  integrates  genome-wide datasets (DNA-seq, RNA-seq, ChIP-seq) provided by the community. This portal is used to query, retrieve, visualize and compare the most up-to-date public data.

A collection of software solutions for pangenome analyses.

To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs.

A catalogue of experimentally-verified pathogenicity, virulence and effector genes involved in the infection of animal, plant, fungal and/or insect hosts.

PhylomeDB is a public database for complete catalogs of gene phylogenie. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.

Pipeline for Cancer Inference

A pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes.

PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. 

Web-interface and database providing tools for the management of different plant phenotyping platforms, and the analysis of images and data.

Providing a data and information resource for individual plant species

Plant-oriented online resource for comparative, evolutionary and functional genomics.

Tool for prediction of disease related mutations in proteins. Tool version 2 (PredictSNP 2) for prediction of disease related mutatins within human genome available since 2016.