What do we do?
At the Computational Evolutionary Genomics Group we are active in the fields of comparative genomics and shotgun metagenomics. We study molecular evolution, develop approaches to genomics data analyses, and implement computational pipelines. We apply evolutionary models to digest sequencing data, and revise these models using the novel data. We study functional genomic elements on the basis of sequence variability among different species and within populations. Our interests range from arthropod genomics, including invertebrate vectors of human pathogens, to the evolution of viruses and clinical microbiology.
Our team’s 2015 highlights are two new bioinformatics resources: BUSCO and CEGA.
BUSCO is an open-source software package for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, i.e. sets of Benchmarking Universal Single-Copy Orthologs derived from OrthoDB. Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences remains mostly limited to technical measures like N50, and now BUSCO addresses this important need from the biological perspective.
CEGA is a catalogue of conserved elements (CNCs/UCEs) derived from multiple genomic alignments. The team identified CNCs independently for five vertebrate clades, each referring to a different last common ancestor and therefore to an overlapping but varying set of CNCs.
Main publications 2015
- Dousse A et al. CEGA-a catalogue of conserved elements from genomic alignments. Nucleic Acids Res. Epub 2015 Nov 2.
- Kriventseva EV et al. OrthoDB v8: update of the hierarchical catalogue of orthologs and the underlying free software. Nucleic Acids Res 2015;43:D250-6.
- Simão FA et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015;31(19):3210-2.