1 SQL, Databases, and Ensembl Modules. 2 Please look for next lecture Ensembl API Tutorial: .
Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl...
Transcript of Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl...
![Page 1: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/1.jpg)
EBI is an Outstation of the European Molecular Biology Laboratory.
Ensembl – An Overview
Twitter: #Ensembl
Dr. Giulietta M. Spudich
Ensembl Outreach
EMBL-EBI
![Page 2: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/2.jpg)
This talk …
Genome Sequencing and Browsers
Ensembl Data
Genes
Variation
Comparative Genomics
Regulation
Access
![Page 3: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/3.jpg)
Beginnings …
1995: 1st free-living organism: bacterium
Haemophilus influenzae (1.8 million bp)
2001: First draft of the human sequence (3 gb)2004: ‘Finished’ human sequence
2014: Polished human sequence with haplotypes (GRCh38)
![Page 4: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/4.jpg)
THOMAS POROSTOCKY; SOURCE:
MEETINGZONE
1000 Genomes Project
ENCODE
Today’s genomics - human
COURTESY OF NIH
![Page 5: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/5.jpg)
5 of 24
Today’s genomics – other species
![Page 6: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/6.jpg)
6 of 24
Ensembl – Access to …
![Page 7: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/7.jpg)
7 of 24
Sister project …
Bacteria, Protists, Plants, Fungi, (non-vertebrate) Metazoa
![Page 8: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/8.jpg)
CGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTC
CGGCCAAAAAAGAACTGCACCTCTGGAGCGGACTTATTTACCAAGCATTGGAGGAATATCG
TAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTGCACTGCTGCGCCTCTGCTG
CGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGA
TTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGA
GCGGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAG
AGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGATTTAGGACCAATA
AGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGCAG
ACTAAAATGGATCAAGCAGATGATGTTTCCTGTCCACTTCTAAATTCTTGTCTTAGAAGAATC
TGAACATAAAAACAACAATTACGAACCAAACCTATTTAAAACTCCACAAAGGAAACCATCTTA
TAATCAGCTGGCTTCAACTCCAATAATATTCAAAGAGCAAGGGCTGACTCTGCCGCTGTAC
CAATCTCCTGTAAAAGAATTAGATAAATTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGT
AGACTAAAAGTCTTCGCACAGTGAAAT
CGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTC
CGGCCAAAAAAGAACTGCACCTCTGGAGCGGACTTATTTACCAAGCATTGGAGGAATATCG
TAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTACTAAAATGGATCAAGCAGAT
GATGTTTCCTGTCCACTTCTAAATTCTTGTCTTAG
AATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGCAGTGAAAGT
CCTGTTGTTCTACAATGTACACATGTAACACCACAAAGAGATAAGTCA
Raw sequence
![Page 9: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/9.jpg)
Ensembl – unlocking the code
06 March 2014 9
Regulation
Gene
Allele
Conserved
sequence
Figure adapted from the ENCODE project www.nature.com/nature/focus/encode/
• Splice variants, proteins, non-coding RNA
• Small and large scale sequence variation, phenotype associations
• Whole genome alignments, protein trees
• Potential promoters and enhancers, DNA methylation
• User upload, custom data
![Page 10: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/10.jpg)
This talk …
Genome Sequencing and Browsers
Ensembl Data
Genes
Variation
Comparative Genomics
Regulation
Access
![Page 11: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/11.jpg)
Challenge: number of gene/protein sequences increases
11 of 24
• UniProtKB/Swiss-Prot (e.g.Q8IU82) 542,258
• UniProtKB/TrEMBL 51,616,950
• NCBI RefSeq (e.g. NP_006570) 37,371,278
![Page 12: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/12.jpg)
Is there a consensus?
• Reaching a consensus coding sequence set for human and mouse.
• Human 29,045 CCDS IDs -18,683 EnsemblGene IDs (e74)
• Mouse 23,093 CCDS IDs- 19,988 EnsemblGeneIDs (e72)
![Page 13: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/13.jpg)
The GENCODE setwww.gencodegenes.org
13 of 24
• Ensembl has long been respected for its high-quality gene sets
• GENCODE genes = Ensembl Automatic Pipeline + Havana Manual Annotation (+ Yale pseudogenes)
• GENCODE is used by ENCODE, 1000 Genomes, and other projects.
![Page 14: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/14.jpg)
This talk …
Genome Sequencing and Browsers
Ensembl Data
Genes
Variation
Comparative Genomics
Regulation
Access
![Page 15: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/15.jpg)
Ensembl Variation
Aims:
• Collect, integrate and annotate all known variants
• Provide tools for comparison to other genomic data
• Provide a framework for access and to improve understanding
![Page 16: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/16.jpg)
Practical applications of variation
Agriculture, livestock breeding• Disease-, insect-, and drought-resistant crops• Healthier, disease-resistant animals• Marker-assisted breeding• More nutritious produce• Reducing the costs of agricultureAnthropology, evolution, and human migration
Molecular and clinical medicine• Diagnosis, detection and treatment:
– e.g. myotonic dystrophy, fragile X syndrome, inherited colon cancer, familial breast cancer
• Pharmacogenomics "custom drugs"
DNA forensics • Identification of suspects
• catastrophe victims• endangered species
![Page 17: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/17.jpg)
Variation Sources
www.ensembl.org/info/genome/variation/sources_documentation
dbSNP (1000 Genomes, ClinVar, etc) ESP (Exome Sequencing Project)UniProt COSMICHGMD_PublicNHGRI-GWAS& more …
![Page 18: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/18.jpg)
Variation in the Browser
![Page 19: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/19.jpg)
Uses an Ensembl gene set to annotate: SNPs Indels Variants in regulatory regions Structural variants
Publication: McLaren et al. 2010 (Bioinformatics)
Ensembl Variant Effect Predictor
Perl scriptWeb interface REST API
XML
NewInterface!
![Page 20: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/20.jpg)
Ensembl Comparative Genomics
Hom
o_sapiens
Pan_tro
glo
dyte
s
Gorilla
_gorilla
Pon
go
_ab
elii
No
ma
scu
s_le
uco
ge
ny
s
Ma
ca
ca
_m
ula
t ta
Ca
llit hrix
_ja
cch
us
Tars
ius_sy
rich
t a
Mic
roce
bu
s_m
uri
nu
s
Oto
lem
ur_
ga
rne
ttii
Tup
aia
_b
ela
ng
eri
Mu
s_m
uscu
lus
Rat t
us_n
orv
eg
icu
s
Dip
odom
ys_
ord
ii
Cavi
a_p
orc
ellu
s
Ict idom
ys_t
ridece
mlin
eatus
Ory
ctola
gus_cunic
ulus
Ochotona_p
rincepsVicugna_pacos
Tursiops_t runcatus
Bos_taurus
Sus_scrofa
Equus_caballusFelis_catus
Ailuropoda_m elanoleuca
Mustela_putorius_furo
Canis_fam iliaris
Myot is_lucifugus
Pteropus_vampyrus
Erinaceus_europaeus
Sorex_araneus
Loxodonta_africana
Proca
via
_capensis
Echin
ops_te
lfairi
Dasy
pu
s_n
ove
mcin
ctu
s
Ch
olo
ep
us_h
offm
an
ni
Mo
no
de
lph
is_d
om
est ic
aM
acro
pu
s_e
ug
en
iiS
arc
op
hilu
s_h
ar ris
i i
Orn
ith
orh
yn
ch
us_a
na
t in
us
Ga
llu
s_g
allu
sM
ele
ag
ris_g
allo
pa
vo
An
as_p
laty
rhy
nch
os
Tae
nio
pyg
ia_g
ut t
ata
Anolis
_caro
linensi
s
Pelo
dis
cus_
sinensi
s
Xenopus_t r
opicalis
Lat imeria
_chalu
mnae
Oreochro
mis_n
ilot ic
us
Tet ra
odon_nigrovirid
is
Takifugu_rubrip
es
Xiphophorus_maculatus
Oryzias_lat ipes
Gasterosteus_aculeatus
Gadus_m orhua
Danio_rerio
Pet romyzon_marinus
Ciona_savignyi
Ciona_intest inalisDrosophila_m
elanogaster
Caenorhabdit is_elegans
Saccharomyces_cerevisiae
Image obtained using Dendroscope (D.H. Huson and C Scornavacca,
Dendroscope 3: An interact ive tool for rooted phylogenet ic t rees and
networks, Syst emat ic Biology, 2012 )
![Page 21: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/21.jpg)
Whole genome alignments
Homo sapiens ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAC-TAGGCG-GCAGAGGCGGAGC--CGCTG-TGGC---ACTGCTGCGCCTCTG-CTGCGCCTCGGGTGTCTTTTGCGGCG
Ancestral sequences ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAC-TAGGCG-GCAGAGGCGGAGC--CGCTG-TGGC---TCTGCTGCGCCTCTG-CTGCGCCTCGGGTGTCTTTTGCGGCG
Pan troglodytes ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAC-TAGGCG-GCAGAAGCGGAGC--CGCTG-TGGC---TCTGCTGCGCCACTG-CTGCGCCTCGGGTGTCTTTTGCGGCG
Ancestral sequences ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAC-TAGGCG-GCAGAGGCGGAGC--CGCTG-TGGC---TCTGCTGCGCCTCTG-CTGCGCCTCGGGTCTCTTTTGCGGCG
Gorilla gorilla gorilla ........................................................................................................................
Ancestral sequences ........................................................................................................................
Pongo abelii ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAC-TAGGCG-GCAGAGGCGGAGC--CGCTG-TGGC---TGTGCTGCACCTGTG-CTGCGCCTCGGGTCTCTTTTGCGGCG
Ancestral sequences ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAT-TAGGCG-GCAGAGGCGGAGC--TGCTG-TGGC--------------TCTG-CTGCGCCTCGGGTCTCTTTTGCGGCG
Macaca mulatta ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAAT-CAGGCG-GCAGAGGTGGAAC--TGCTGCTGGC--------------TCTG-CTGCGCCTCGGGTCTCTTTTGCGGCG
Ancestral sequences ACGT-GG--CCAGCGCGGGCTTGTGGCGCGAGCGTCTGAAAT-GAGGCG-GCAGAGGCGGAGC--TGCTG-TGGC--------------TCTG-CCGCGCCTCGGGTCTTTTCTGCGGCG
Callithrix jacchus ACGT-GG--TCAGCGCGGGCTTGTGGCGCGAGCGTCTGAAAT-GAGGCG-GCAGAGGCGGACC--TGCTG-TGTC--------------TCTG-CCGCGCCTCCGGTCTTTTCTGCGACG
Ancestral sequences ACGT-GC--CGAGAGCGGGCTTTTGGCGCGAGCGTCTGAAAT-AAGGCG-GCGGAGGCGGAGC--TGCTG-CGGCT------------------CCGCGTCTCGGGTCTTTTCTGCGGCA
Mus musculus ACGG-GC--AGAGCGCGGGCTTTTCGCGGGAGCGGGAGCCGT-G----------AGGCGTTGCCGTCAGT-CAGCT-----------------ACCGCTGC-------------------
Ancestral sequences ACGG-GC--AGAGCGCGGGCTTTTCGCGGGAGCGTGAGAAGT-G----------AGGCGGTGCCGTCCGT-CAGCT-----------------ACCGCAAC-------------------
Rattus norvegicus ACGGCGC--AGAGCGCGGGCTTTTCGCAGGAGCGTGAGAAGT-G----------AGGCGGCGCCGTCCGT-CAGCG-----------------GCCGCAAC-------------------
Ancestral sequences ACGT-GC--CGAGAGCGGGCTTTTGGCGCGAGCGTCTGAAAT-AAGGCG-GCGGAGGCGGAGC--TCCTT-CAGCT------------------CCGCGTCTCGGGTCTTTTCTGCGGCA
Oryctolagus cuniculus ACGT-GC--CCAGAGCGGGCTTTTGGCGCGAGCGTCTGAAAA-AAGGCT-ATGGAGGCGGAGC--TCCTT-CAGCT------------------CCGCGTCTGGGGTCTTGCCTAGGGCA
Ancestral sequences ACGT-GC--CGAGAGCGGGCTTTTGGCGCGAGCGTCTGAAAT-AAGGCG-GCGGAGGCGGAGC--TGCTG-CGGCT------------------CCGCGTCTCGGGTCTTTTCTGCGGCA
Bos taurus ACAT-ATCCCGAGAGCAGGCTTTTGGCGCGAGAATCTGAAAC-CCGGTGGGCGGAGGTGCGGC--TGCTG-AAGTTTG----------------C--TGTCTCGGGCGG-T---------
Ancestral sequences ACGT-GCTCCGAGAGCGGGCTTTTGGCGCGAGCGTCTGAAAT-AAGGCGAGCGGAGGCGGAGC--TGCTG-GGGCTCC----------------C--TGTCTCGGGTGG-TTCTGTGGCA
Canis lupus familiaris ........................................................................................................................
Ancestral sequences ........................................................................................................................
Equus caballus ACGT-GCTCAGAGAGCGGGCTTTTGGCGCGAGCGTCTGAAAAGAAGGCAAGCGGAGGCGGAGT--TGCTG-GGGCTCC----------------C--TGACTGGGGTGG-TTGTGTGGCA
Great apes
Old world
monkeys
Primates
Glires
Rodents
Laurasiatheria
Boroeutherian
![Page 22: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/22.jpg)
This talk …
Genome Sequencing and Browsers
Ensembl Data
Genes
Variation
Comparative Genomics
Regulation
Access
![Page 23: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/23.jpg)
Gene expression:The basic model
Transcription Factor Binding Sites Promoter Gene
mRNA
Transcription Factors Activation
Repression RNA polymerase complex
2 nm
![Page 24: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/24.jpg)
Available data
![Page 25: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/25.jpg)
Regulation (ENCODE + …)
![Page 26: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/26.jpg)
This talk …
Genome Sequencing and Browsers
Ensembl Data
Genes
Variation
Comparative Genomics
Regulation
Access
![Page 27: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/27.jpg)
Open source- access our data!
• Ensembl Views (Website, ftp)
• Ensembl Database (Perl API, REST API, MySQL)
• BioMart – Quick Data Retrieval (Web interface , Bioconductor, Galaxy, BioMaRt)
![Page 28: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/28.jpg)
Ensembl is used worldwide
Top users:
UK
US
Canada
China
France
Germany
Italy
Japan
Spain
![Page 29: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/29.jpg)
EBI is an Outstation of the European Molecular Biology Laboratory.
Workshops Worldwide (2013)
![Page 30: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/30.jpg)
EBI is an Outstation of the European Molecular Biology Laboratory.
What’s coming? (2014)
New Assemblies:
• GRCh38 (and all the updated annotation)www.ensembl.info/blog (category GRCh38)
• Baboon
• Vervet monkey
• Amazon molly
• Crab eating macaque (Pre.ensembl.org)
• Hedgehog (Pre.ensembl.org)
New BLAST
New Regulatory Buildwww.ensembl.info/blog/2013/12/26/the-new-ensembl-regulatory-annotation
![Page 31: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/31.jpg)
Learn more
• Comments and questions? [email protected]
• YouTube channel www.youtube.com/user/EnsemblHelpdesk
• Mailing lists [email protected], [email protected]
• Courses online www.ensembl.info/ecourse
• Our tutorials page www.ensembl.org/info/website/tutorials
![Page 32: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/32.jpg)
Follow us• Facebook www.facebook.com/Ensembl.org
• Twitter https://twitter.com/Ensembl
• Come visit our blog! www.ensembl.info
![Page 33: Ensembl An Overview - European Bioinformatics Institute...Ensembl –An Overview Twitter: #Ensembl Dr. Giulietta M. Spudich Ensembl Outreach EMBL-EBI. ... MEETINGZONE 1000 Genomes](https://reader036.fdocuments.us/reader036/viewer/2022063018/5fddde0f9b097d434575562f/html5/thumbnails/33.jpg)
Acknowledgements
FundingEuropean Commission Framework Programme 7