Ensembl Ensembl GenomesGenomes extending Ensembl across extending Ensembl across

the taxonomic spacethe taxonomic space

Amer Talal Wazwaz106316@ppu.edu

wazwazamer@yahoo.com

21/3/2011

Ensembl GenomesEnsembl Genomes httphttp://://wwwwww..ensemblgenomesensemblgenomes..orgorg//

since April 2009since April 2009

An extension of ensemblAn extension of ensembl

since July2000since July2000

Developed jointly byDeveloped jointly by EBI EBI and and

WellcomeWellcomeTrustTrust

SangerSanger InstituteInstitute

IntroductionIntroduction  What is Ensembl GenomesWhat is Ensembl Genomes

New portal offering integrated access to genome-scale New portal offering integrated access to genome-scale data for data for non-vertebratenon-vertebrate species, developed using the species, developed using the

Ensembl genome annotation and visualization platformEnsembl genome annotation and visualization platform

Consists of five Consists of five sub-sub-portalsportals

( ( for for bacteriabacteria, , protistsprotists, , fungifungi, , plantsplants and and invertebrate invertebrate metazoametazoa ) )

designed to designed to complement thecomplement the availability of availability of vertebratevertebrate genomes in Ensemblgenomes in Ensembl..

Ensembl GenomesEnsembl Genomes httphttp://://wwwwww..ensemblgenomesensemblgenomes..orgorg//

Each site contains data for selected species from Each site contains data for selected species from their domain, chosen for their scientific interesttheir domain, chosen for their scientific interest..Information is available about each species, including theInformation is available about each species, including the

assembly versionassembly version and and annotation methodsannotation methods used, the used, the overall overall composition of the genomecomposition of the genome

Statement of NeedStatement of NeedIn response to the need of creating annotated genome In response to the need of creating annotated genome

databasesdatabases

To represent the best annotation for every To represent the best annotation for every genomegenome

THRO UGHTHRO UGH

Working with all sections of the relevant scientific Working with all sections of the relevant scientific communitycommunity

The browser offers a number of views of locations in the genome, genes, and specific transcripts

location view for a

region of a chromosome

gene view

transcript view

Statement of Need Statement of Need  Main functionalityMain functionality

Portals offer access to a graphical view of each genome, using the Ensembl Portals offer access to a graphical view of each genome, using the Ensembl genome browser softwaregenome browser software..

Graphical Karyotype

Views

NonbacterialNonbacterial BacterialBacterial

Data Nature of the DBData Nature of the DB

ENA/GenBank/DDBJ

Gramene

TAIR

NASC

IGGP

ENA/GenBank/DDBJ

Saccharomyces Genome Database

GeneDB

Central Aspergillus Data Repository

ENA/GenBank/DDBJ

FlyBase

WormBase

VectorBase

Drosophila Population Genome Project

ENA/GenBank/DDBJ

Regulon DB

ENA/GenBank/DDBJ

PlasmoDB

EBI staff active participants in their primary annotationCollaborators to build Ensembl databasesImporting canonical data from an authority for a given speciesRecords previously submitted to the ENA/GenBank/DDBJ

public nucleotide archives

Supplemented by protein functional annotation from UniProtKB

Methods of Data Methods of Data RetrievalRetrieval Ensembl Genomes data is available Ensembl Genomes data is available

throughthrough BioMart data warehousing system

(API )Perl

These interfaces are supported by a number of relational (MySQL) (RDBMS)(RDBMS) database schemas

“efficient high-level access“

That run as a server providing multi-user access toThat run as a server providing multi-user access to

Core databases describing sequence, features and stable identifiers

Additional databases for other certain types of data

Added ToolsAdded Tools Assembly ConverterAssembly Converter

Map your data to the current assemblyMap your data to the current assembly..

ID History ConverterID History ConverterConvert a set of Ensembl IDs fromConvert a set of Ensembl IDs from

a previous release into their current equivalentsa previous release into their current equivalents..

Variant Effect PredictorVariant Effect Predictor ((Formerly SNP Effect PredictorFormerly SNP Effect Predictor))

This tool takes a list of variant positions and This tool takes a list of variant positions and alleles, and predicts the effects of each alleles, and predicts the effects of each of these on any overlapping features of these on any overlapping features (transcripts, regulatory features) (transcripts, regulatory features)

annotated in Ensemblannotated in Ensembl..

Short TutorialShort Tutorial Search for a certain Search for a certain genegene

We will get a list of We will get a list of the matched gene the matched gene in different speciesin different species

At the top of the page At the top of the page there are 3 tabsthere are 3 tabsLocationLocation

GeneGene ProteinProtein

Graphical alignment Graphical alignment of gene of interestof gene of interest

Short TutorialShort TutorialThe gene of interest The gene of interest highlighted against the highlighted against the genomic contiggenomic contig

Adjacent genes on eitherAdjacent genes on either sides are shownsides are shown

Short TutorialShort TutorialGenomic Genomic location location pagepage

Graphical Graphical representatirepresentation of proteinon of protein

Short TutorialShort Tutorial

Useful Useful informatiinformation at theon at the sub-gene sub-gene summary summary page tabspage tabs

Thank YouThank You

QuestionsQuestions