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EMBL-EBI Powerpoint Presentation


EBI is an Outstation of the European Molecular Biology Laboratory.  

EBI patent related services 

Jennifer McDowall

Senior Scientist, EMBL-EBI 

3rd Annual

Forum for SMEs 

September 3-4th 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 

EBI patent related services


EMBL 

Know the Data��Nucleotides 

EBI patent related services 

    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 

   

EBI patent related services


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)
 

     

 


EBI patent related services 

EMBL Patent Sequence Entry 

Version, dates, archive 

Patent number, title, link to patent


 

UniProt 

Know the Data��Proteins 

    Release and updates

EBI patent related services

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)
 

EBI patent related services 

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


EBI patent related services 

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     

EBI patent related services


EMBL sequence version archive (SVA) 

EBI patent related services 

View old entries 

Enter accession #


EBI patent related services 

Sequence record from EMBL SVA


EBI patent related services 

Comparing versions in EMBL SVA 

Select and compare versions


EBI patent related services


EBI patent related services 

UniProtKB sequence annotation version server - UniSave 

Enter accession #


EBI patent related services 

UniSave results 

Select and compare versions 

View old entries


EBI patent related services 

Searching the databases��


EB-eye search by patent number 

Search for patent WO0146262 

EBI patent related services


EB-eye search by patent number 

EBI patent related services


EBI patent related services 

EB-eye nucleotide sequences from WO0146262


Sequence Similarity Search Tools 

EBI patent related services 

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


EBI patent related services 

Fasta v. patent protein sequences


Tools:  Genomes & Proteomes FASTA 

EBI patent related services


Database size 

Query length 

FASTA 

WU-BLAST 

NCBI BLAST 

PSI-SEARCH 

When to use which search? 

EBI patent related services


PDB Swiss-Prot UniRef50 UniRef 90 UniRef100 UniProtKB UniParc  

FASTA 

WU-BLAST 

NCBI BLAST 

PSI-SEARCH 

time to search 

When to use which search? 

EBI patent related services


InterProScan protein signature search 

EBI patent related services 

www.ebi.ac.uk/interpro/


InterPro signature database 

EBI patent related services


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 

EBI patent related services


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 

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 

EBI patent related services 

#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/


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