Ensembl 2008

Abstract

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Characterization of drCol 15a1b: A Novel Component of the Stem Cell Niche in the Zebrafish Retina

“…(polychaete annelid worm), Daphnia pulex (water flea, anarthropod), Trichoplax adhaerens (placozoan), Helobdella robusta (leech, annelid), Branchiostoma floridae (amphioxus, cephalochordate), and Nematostella vectensis (cnidarian). Additionally, the lamprey proteome was searched via the Ensembl release 50 [39]. Protein models hit with low E-values were considered potential collagen XV/XVIII peptides.…”

Characterization of the intronic portion of cadherin superfamily members, common cancer orchestrators

“…Selection of cadherin and non-cadherin genes across species -the seven-domain approach Using the Ensembl database (v52, v60) 15 and InterPro annotation of protein domains, 16 a keyword search was performed in order to obtain all domains that are present within cadherins from six species that have an extensive genomic infrastructure (such as expressed sequence tag (EST) and cDNA collections) and high coverage after genome sequencing/assembly: Homo sapiens, Mus musculus, Gallus gallus, Danio rerio, Xenopus tropicalis and Ciona intestinalis. These six species provide a general view on chordate evolution starting from C. intestinalis (commonly used to explore the evolutionary origins of the chordate lineage 17 ) up to H. sapiens.…”

“…To determine intronic sequence conservation within cadherin and non-cadherin introns, all available data on mammalian conservation from the Ensembl database 15 was used. The frequency of genomic evolutionary rate profiling (GERP) constrained elements across 12 mammalian species was analysed to inquire intronic sequence conservation (obtained using Ensembl's EnredoPecan-Ortheus pipeline on 12 eutherian mammals 20 ).…”

“…13,15 We combined literature data and protein domain databases (InterPro 16 ) to collect genes that coded for protein sequences currently classified as cadherins from six distinct genomes, resulting in seven distinct cadherin-related InterPro domains. Selected genes were further curated to assure that only protein-coding genes were selected and included in data set A (Supplementary Table 1).…”

“…We compared the intronic sequence conservation (Genomic Evolutionary Rate Profiling constrained elements) across 12 mammalian species 15,31 by studying 3 separated groups of human introns: (1) cadherin introns (data set A); (2) non-cadherin introns; and (3) 1000 data sets of 1000 randomly chosen non-cadherin introns (random data set). Sequence conservation was analysed by separating all cadherin and non-cadherin introns into three length classes, each encompassing the same number of nucleotides.…”