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EBI patent related services

EBI patent related services. 3 rd Annual Forum for SMEs. September 3-4 th 2009. Jennifer McDowall Senior Scientist, EMBL-EBI. Overview. Databases available Sequence archives Searching the database. EBI patent related services. Databases available…. EBI patent related services.

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EBI patent related services

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  1. EBI patent related services 3rd Annual Forum for SMEs September 3-4th 2009 Jennifer McDowall Senior Scientist, EMBL-EBI

  2. Overview • Databases available • Sequence archives • Searching the database EBI patent related services

  3. Databases available… EBI patent related services

  4. USPTO JPO GenBank DDBJ September 2009nucl >9.4m sequencesprot > 2.5m sequences EMBL EPO policy: data released topublic (and to EMBL) 18 months after the patent application date, independent of whether patent has been granted. . EPO Sequence data from patent literature EBI patent related services

  5. Know the Data…Nucleotides EMBL • Release and updates EBI patent related services

  6. Know the Data…Nucleotides EMBL Release and updates • Divided into classes and divisions... 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

  7. Know the Data…Nucleotides EMBL Release and updates • Divided into classes and divisions... 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 EBI patent related services

  8. Know the Data…Nucleotides EMBL Release and updates Divided into classes and divisions... • Supplementary sets: • EMBL-CDS, EMBL-MGA • Specialist databases: • Immunoglobulins (IMGT/HLA, IMGT/LIGM) • Alternative splicing (ASDT) • Completed proteomes (Ensembl, Integr8) • Variation (HGVBase, dbSNP) EBI patent related services

  9. EMBL Patent Sequence Entry Version, dates, archive Patent number, title, link to patent EBI patent related services

  10. EBI patent related services Know the Data…Proteins UniProt • Release and updates

  11. Know the Data…Proteins UniProt Release and updates Divided into 3 sections: UniProtKB UniParc UniRef • Taxonomic info • Annotated sequence • Combines sequences by % ID • UniRef100, 90, 50 • Protein archive • Covers ALL proteins (including UniMess) SwissProt TrEMBL Automatic annotation Manual annotation EBI patent related services

  12. Know the Data…Proteins UniProt Release and updates Divided into 3 sections • 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

  13. Bulk download http://www.ebi.ac.uk/patentdata/ Nucleotide sequences Protein sequences EBI patent related services

  14. Bulk download ftp.ebi.ac.uk/pub/databases/embl/patent/ EBI patent related services

  15. Sequence archives… EBI patent related services

  16. Sequence archives • EMBL nucleotide sequence version archive (SVA)www.ebi.ac.uk/embl/sva • UniSave – UniProt sequence/annotation version archivewww.ebi.ac.uk/uniprot/unisave EBI patent related services

  17. Enter accession # View old entries EMBL sequence version archive (SVA) EBI patent related services

  18. Sequence record from EMBL SVA EBI patent related services

  19. Select and compare versions Comparing versions in EMBL SVA EBI patent related services

  20. EBI patent related services

  21. UniProtKB sequence annotation version server - UniSave Enter accession # EBI patent related services

  22. Select and compare versions View old entries UniSave results EBI patent related services

  23. Searching the databases… EBI patent related services

  24. EB-eye search by patent number Search for patent WO0146262 EBI patent related services

  25. EB-eye search by patent number EBI patent related services

  26. EB-eye nucleotide sequences from WO0146262 EBI patent related services

  27. Sequence Similarity Search Tools Toolbox PSI search BLAST FASTA Smith-Waterman PSI-BLAST Wu-BLAST FASTA suite MPsrch PSI-SEARCH NCBI-BLAST ScanPS SSEARCH EBI patent related services

  28. Blast v. patent nucleotide sequences

  29. Fasta v. patent protein sequences EBI patent related services

  30. Tools: Genomes & Proteomes FASTA EBI patent related services

  31. When to use which search? NCBI BLAST Query length WU-BLAST PSI-SEARCH FASTA Database size EBI patent related services

  32. When to use which search? NCBI BLAST time to search WU-BLAST PSI-SEARCH FASTA PDB Swiss-Prot UniRef50 UniRef 90 UniRef100 UniProtKB UniParc EBI patent related services

  33. InterProScan protein signature search www.ebi.ac.uk/interpro/ EBI patent related services

  34. InterPro signature database EBI patent related services

  35. Some search guidelines… EBI patent related services

  36. Search Guidelines #1 Use the most appropriate tool for your search - Don’t assume one tool will cater to all your search needs NCBI BLAST Query length WU-BLAST PSI-SEARCH FASTA Database size EBI patent related services

  37. 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

  38. 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... #6 Don’t assume homologues have the same function #5 Change parameters when necessary (gap penalties, scoring matrices...) • Orthologs have similar functions • Paralogs acquire different functions EBI patent related services

  39. 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... #6 Don’t assume homologues have the same function #5 Change parameters when necessary (gap penalties, scoring matrices...) #7 Use multiple sequence alignments to validate relatedness #8 Consider filtering low complexity regions EBI patent related services

  40. Typical workflow search Check stats review function evolution compare EBI patent related services

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

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