EBI is an Outstation of the European Molecular Biology Laboratory.
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Jennifer McDowallSenior Scientist, EMBL-EBI
3rd Annual Forum for SMEs
September 3-4th 2009
Overview
Databases available
Sequence archives
Searching the database
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Databases available…
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September 2009nucl > 9.4m sequencesprot > 2.5m sequences
GenBankGenBank
EMBLEMBL
DDBJDDBJ
EPOEPO
USPTOUSPTO JPOJPO
EPO policy: data released topublic (and to EMBL) 18 months after the patent application date, independent of whether patent has been granted.
.
Sequence data from patent literature
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EMBLEMBL
Know the Data…Nucleotides
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Release and updates
EMBLEMBL
Know the Data…Nucleotides
Divided into classes and divisions...
Release and updates
ANN – Annotated Constructed Seq PAT – Patent
CON – Constructed Sequence STS – Sequence Tagged Site
EST – Expressed Sequence Tag STD – Standard
GSS – Genome Survey Sequence TPA – Third Party Annotation
HTC – High Throughput cDNA TSA – Transcriptome Shotgun Assembly
HTG – High Throughput Genome WGS – Whole Genome Shotgun
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EMBLEMBL
Know the Data…Nucleotides
Divided into classes and divisions...
Release and updates
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HUM – Human
MUS – Mouse
ROD – Rodent (excluding mouse)
MAM – Mammal (excluding human, mouse, rodent)
VRT – Vertebrate (excluding human, mouse, rodent, mammal)
FUN – Fungi PRO – Prokaryote ENV – Environment
INV – Invertebrate PHG – Phage SYN – Synthetic
PLN – Plant VIR – Viral TGN – Transgenic
UNC – Unclassified
EMBLEMBL
Know the Data…Nucleotides
Divided into classes and divisions...
Release and updates
Supplementary sets: EMBL-CDS, EMBL-MGA
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Specialist databases: • Immunoglobulins (IMGT/HLA, IMGT/LIGM)
• Alternative splicing (ASDT)
• Completed proteomes (Ensembl, Integr8)
• Variation (HGVBase, dbSNP)
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EMBL Patent Sequence Entry
Version, dates, archive
Patent number, title, link to patent
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UniProtUniProt
Know the Data…Proteins
Release and updates
UniProtUniProt
Know the Data…Proteins
Divided into 3 sections:
Release and updates
UniProtKBUniProtKB
• Taxonomic info • Annotated sequence
UniRefUniRef
• Combines sequences by % ID
• UniRef100, 90, 50
UniParcUniParc
• Protein archive• Covers ALL proteins (including UniMess)
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SwissProt TrEMBL
Manual annotation
Automatic annotation
UniProtUniProt
Know the Data…Proteins
Divided into 3 sections
Release and updates
Specialist databases linked to UniProt: • Structure (PDBe, SGT)
• Immunoglobulins (IMGT/HLA)
• Alternative splicing (ASDT)
• Completed proteomes (Ensembl, Integr8)
• Protein interactions (IntAct)
• Protein signatures (InterPro)
• Patent proteins (EPO, USTPO, JPO, KIPO)
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Bulk download
http://www.ebi.ac.uk/patentdata/
Nucleotide sequences
Protein sequences
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Bulk download
ftp.ebi.ac.uk/pub/databases/embl/patent/
Sequence archives…
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• EMBL nucleotide sequence version archive (SVA)www.ebi.ac.uk/embl/sva
• UniSave – UniProt sequence/annotation version archivewww.ebi.ac.uk/uniprot/unisave
Sequence archives
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EMBL sequence version archive (SVA)
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View old entries
Enter accession
#
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Sequence record from EMBL SVA
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Comparing versions in EMBL SVA
Select and compare versions
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UniProtKB sequence annotation version server - UniSave
Enter accession
#
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UniSave results
Select and compare versions
View old entries
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Searching the databases…
EB-eye search by patent number
Search for patent WO0146262
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EB-eye search by patent number
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EB-eye nucleotide sequences from WO0146262
Sequence Similarity Search Tools
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Toolbox
BLASTBLAST
NCBI-BLASTNCBI-BLAST
Wu-BLASTWu-BLAST
FASTAFASTA
FASTA suiteFASTA suite
Smith-WatermanSmith-Waterman
MPsrchMPsrch
ScanPSScanPS
SSEARCHSSEARCH
PSI searchPSI search
PSI-SEARCHPSI-SEARCH
PSI-BLASTPSI-BLAST
Blast v. patent nucleotide sequences
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Fasta v. patent protein sequences
Tools: Genomes & Proteomes FASTA
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Database size
Que
ry le
ngth
FASTA
WU-BLAST
NCBI BLAST
PSI-SEARCH
When to use which search?
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PDB Swiss-Prot UniRef50 UniRef 90 UniRef100 UniProtKB UniParc
FASTA
WU-BLAST
NCBI BLAST
PSI-SEARCH
time
to s
earc
hWhen to use which search?
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InterProScan protein signature search
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www.ebi.ac.uk/interpro/
InterPro signature database
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Some search guidelines…
Search Guidelines
#1 Use the most appropriate tool for your search
- Don’t assume one tool will cater to all your search needs
Database size
Que
ry le
ngth
FASTA
WU-BLAST
NCBI BLAST
PSI-SEARCH
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Search Guidelines
#1 Use the most appropriate tool for your search
#2 Best search option protein seq v. protein DB
2nd translated DNA seq v. protein DB
3rd DNA seq v. DNA DB
Worst protein seq v. transl DNA BD
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Search Guidelines
#1 Use the most appropriate tool for your search
#2 Best search option protein seq v. protein DB
#3 Search the smallest DB likely to have your sequence
#4 Check statistics – histograms...
#5 Change parameters when necessary (gap penalties, scoring matrices...)
#6 Don’t assume homologues have the same function
• Orthologs have similar functions
• Paralogs acquire different functions
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Search Guidelines
#1 Use the most appropriate tool for your search
#2 Best search option protein seq v. protein DB
#3 Search the smallest DB likely to have your sequence
#4 Check statistics – histograms...
#5 Change parameters when necessary (gap penalties, scoring matrices...)
#6 Don’t assume homologues have the same function
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#7 Use multiple sequence alignments to validate relatedness
#8 Consider filtering low complexity regions
Typical workflow
searchreview Check stats
compareevolutionfunction
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EBI is an Outstation of the European Molecular Biology Laboratory.
Contacts:http://www.ebi.ac.uk/support/