Ensembl comparative genomics resources

Abstract

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.Database URL: http://www.ensembl.org.

High-Throughput Sequencing Technologies and new Approaches in Food Microbiology

“…Metagenomics allows the analysis of whole-genome sequences of DNA extracted from an organism, in which bioinformatic tools are used to individuate differences between the sequences [8]. It is an extremely powerful method that can be adopted to describe the genetic potential of several kinds of microbiome, and includes two fundamental approaches: the amplicon sequencing method, that uses the high-throughput 16S rRNA gene regions, and the shoutgun method which concerns the coverage of the genome outside of the small 16S rRNA gene region and this means that specific, strain level discrimination is achievable [9].…”

Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection

“…Analysis of a gene gain/loss tree of 70 animal species through the Ensembl Compara utility [22,23] indicated that a single G6PC gene is present in the Drosophila genome, whereas lamprey (Petromyzon marinus, Cyclostomata) displays two genes and most bony fishes, birds, reptiles, amphibians and mammals have at least three paralogs. Possibly due to gene loss, no G6PC gene is described in the two Tunicata genomes included in the Ensembl Compara dataset.…”

Recent advances in computational epigenetics

“…3,4 Genetic and genomic attributes have been studied in detail, and current knowledge is captured in databases, which include ENCODE, Ensembl, Gene, GEO and GWAS for humans, as well as other organism-specific examples. [5][6][7][8][9] The collated data are extensive and draw heavily both on state-of-the-art methods of gene sequencing and on extensive gene expression measurements, providing a basis for investigation of molecular evolution, disease-specific mutations and other. Despite this wealth of data, however, it is now clear that gene factors alone are insufficient to explain the complex mechanisms producing diversity and heritable changes in phenotype.…”