EMBL-EBI Powerpoint Presentation

EBI is an Outstation of the European Molecular Biology Laboratory.  

EBI patent related services 

Jennifer McDowall

Senior Scientist, EMBL-EBI 

3^rd Annual

Forum for SMEs 

September 3-4^th 2009

Overview 
 

• Databases available

• Sequence archives 
  

• Searching the database 
  

 

EBI patent related services

Databases available… 

EBI patent related services

   September 2009 
nucl  > 9.4m sequences 
prot  > 2.5m sequences 

GenBank 

EMBL 

DDBJ 

EPO 

USPTO 

JPO 

EPO policy:  data released  to 
public (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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EMBL 

Know the Data…Nucleotides 

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Release and updates

EMBL 

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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EMBL 

Know the Data…Nucleotides 

Divided into classes and divisions... 

Release and updates 

EBI patent related services 

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

EMBL 

Know the Data…Nucleotides 

Divided into classes and divisions... 

Release and updates 

Supplementary sets:  

EMBL-CDS, EMBL-MGA 
 

EBI patent related services 

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

 

UniProt 

Know the Data…Proteins 

Release and updates

UniProt 

Know the Data…Proteins 

Divided into 3 sections:  

Release and updates 

UniProtKB 

• Taxonomic info
• Annotated sequence

 

UniRef 

• Combines sequences   by % ID
• UniRef100, 90, 50

 

UniParc 

• Protein archive
• Covers ALL proteins                      (including UniMess)

 

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SwissProt 

TrEMBL 

Manual annotation 

Automatic annotation

UniProt 

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)

 

  
 

EBI patent related services

EBI patent related services 

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… 

EBI patent related services

• EMBL nucleotide sequence version archive (SVA) 
  www.ebi.ac.uk/embl/sva 
  

• UniSave – UniProt sequence/annotation version archive 
  www.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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EBI patent related services 

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 

EBI patent related services

EBI patent related services 

EB-eye nucleotide sequences from WO0146262

Sequence Similarity Search Tools 

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Toolbox 

BLAST 

NCBI-BLAST 

Wu-BLAST 

FASTA 

FASTA suite 

Smith-Waterman 

MPsrch 

ScanPS 

SSEARCH 

PSI search 

PSI-SEARCH 

PSI-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 

Query length 

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 search 

When 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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EBI patent related services 

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 

Query length 

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 

2^nd  translated DNA seq v. protein DB

3^rd  DNA seq v. DNA DB

Worst  protein seq v. transl DNA BD 

EBI patent related services

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

 

EBI patent related services

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 

search 

review 

Check stats 

compare 

evolution 

function 

EBI patent related services

EBI is an Outstation of the European Molecular Biology Laboratory.  

Contacts: 
http://www.ebi.ac.uk/support/