Suite of services for the assembly, archiving, and analysis of microbiome-derived sequence data
Section Head, Team Leader and Senior Scientist
Microbiome Informatics
rdf [at] ebi.ac.uk
ORCID: 0000-0001-8626-2148
EditOur services use complex mathematical models tailored for life-science research. For example, the HMMER algorithm offers fast detection of distantly related proteins and is available through our website infrastructure. We aim to simplify access to curated, complex data, and to maximise biological knowledge by extending annotation based on sequence similarity.
Our MGnify service enables researchers to submit sequence data and associated descriptive metadata about environmental samples to public nucleotide archives. Once deposited, our team helps ensure the data is functionally analysed (using an InterPro-based pipeline), taxonomically analysed and visualised via a web interface.
This graphic shows the workflow for our metagenomics analysis.
We participate in EMBL-EBI’s Training Programme, offering courses in metagenomics and other approaches to sequence analysis.
We welcome new collaborations in all areas, and are particularly interested in working with people who have developed new tools for analysis, or who are working with metagenomics datasets generated with new sequencing technology.
The Ensembl project, founded in 1999 to support the results of the Human Genome Project, supports over 80 vertebrate species and provides resources such as reference gene sets, whole genome alignments, gene homology annotation, gene sequence alignments, variant annotation and regulatory regions. Man…
Map your data to the current assembly. Based on the CrossMap tool
Ensembl Genomes is an integrating portal providing access to genome-scale data from across the taxonomic space. Using the same infrastructure developed in the context of the vertebrate-focused Ensembl project, it offers consistent interactive and programmatic user interfaces to data from important i…
Searches Ensembl Bacteria sequences using NCBI-BLAST
Convert a set of Ensembl IDs from a previous release into their current equivalents
Searches Ensembl Bacteria sequences using Exonerate
Upload a set of SNPs in our standard format and export a file containing consequence types
Map your data to the current assembly
Searches Ensembl Fungi sequences using BLAST
Get a subset of data from a BAM | VCF file
Convert a set of Ensembl IDs from a previous release into their current equivalents
Searches Ensembl Fungi sequences using Exonerate
Upload a set of SNPs in our standard format and export a file containing consequence types
Map your data to the current assembly
Get a subset of data from a BAM | VCF file
Convert a set of Ensembl IDs from a previous release into their current equivalents
Searches Ensembl Metazoa sequences using Exonerate
Upload a set of SNPs in our standard format and export a file containing consequence types
Map your data to the current assembly
Search Ensembl Plants sequences with NCBI-BLAST
Get a subset of data from a BAM | VCF file
Convert a set of Ensembl IDs from a previous release into their current equivalents
Search Ensembl Plants sequences with Exonerate
Upload a set of SNPs in our standard format and export a file containing consequence types
Map your data to the current assembly
Searches Ensembl Protists sequences using NCBI-BLAST
Get a subset of data from a BAM | VCF file
Convert a set of Ensembl IDs from a previous release into their current equivalents
Searches Ensembl Protists sequences using Exonerate
Upload a set of SNPs in our standard format and export a file containing consequence types