Ensembl genome
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Transcript of Ensembl genome
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Ensembl Ensembl GenomesGenomes extending Ensembl across extending Ensembl across
the taxonomic spacethe taxonomic space
Amer Talal [email protected]
21/3/2011
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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
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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..
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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
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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
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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
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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
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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
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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..
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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
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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
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Short TutorialShort TutorialGenomic Genomic location location pagepage
Graphical Graphical representatirepresentation of proteinon of protein
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Short TutorialShort Tutorial
Useful Useful informatiinformation at theon at the sub-gene sub-gene summary summary page tabspage tabs
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Thank YouThank You
QuestionsQuestions