EBI services. Jennifer McDowall EMBL-EBI
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1 EBI services Jennifer McDowall EMBL-EBI The SLING project is funded by the European Commission within Research Infrastructures of the FP7 Capacities Specific Programme, grant agreement number (Integrating Activity)
2 Website: EB-eye Search all main databases in one go Thematic index
3 Website: Databases Patent resources Sequences Genomes Chemistry Structures Gene expression Reactions & pathways Literature Training elearning Workshops 2Can education resource Tools Sequence searching Sequence analysis Structural analysis Functional analysis Industry programme Industry support SME Support
4 searching EBI...
5 Sequence data from patent literature USPTO GenBank DDBJ JPO + KIPO INSDC agreement: Free unrestricted access Permanently accessible All data exchanged daily ENA EPO EPO policy: Data publically released 18 months after patent application date (whether patent granted or not) October 2010 patent nucleotides > 17.5m sequences patent proteins > 4.9m sequences
6 Patent resources at EBI
7 Patent sequence records at EBI ENA (formerly EMBL-Bank) UniParc (division of UniProt) NR patent sequences >124 million sequences patent + non-patent nucleotides redundant non-patent sequence prior art searches >24 million sequences patent + non-patent proteins non-redundant patent sequence patent proteins and nucleotides non-redundant prior art searches additional patent annotation
8 Non-redundant patent databases ENA (redundant) Remove sequence redundancy Level-1 NR Group by patent families Additional annotation, including priority dates for patent families Level-2 NR
9 Searching for sequence simple EB-eye search...
10 EB-eye search by patent number Search for patent WO
11 EB-eye search by patent number Search for WO
12 EB-eye search by patent number Search for WO Databases with sequence data for WO Literature for WO
13 EB-eye search by patent number Search for WO WO literature and sequence databases
14 EB-eye search by patent number Search for WO WO literature and sequence databases Lists nucleotide sequences from WO
15 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences
16 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO nucleotide sequence record in ENA
17 Patent sequence record in ENA Sequence version Navigate to related data e.g. Version archive Download data Dates (first public and last updated) Graphical viewer DNA source Patent reference Navigate to external data sources e.g. UniProt Sequence
18 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences ENA sequence record
19 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO literature ENA sequence record
20 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO literature ENA sequence record
21 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO literature WO in CiteXplore ENA sequence record
22 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO in CiteXplore WO literature ENA sequence record
23 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO in CiteXplore WO literature WO in ENA sequence record
24 EB-eye search by patent number Search for WO WO literature and sequence databases WO sequences WO in CiteXplore WO literature WO in ENA sequence record
25 Searching for sequence advanced text search...
26 SRS for more search options 1 st : Select resources to search 2 nd : Create query
27 SRS for more search options Select library tab
28 SRS for more search options Search >100 databases Select library tab Patent literature Patent DNA Patent proteins
29 SRS for more search options Select library tab Here, selected NR-level 2 DNA database
30 SRS for more search options Select library tab Select resources to search
31 SRS for more search options Select library tab Select resources to search 1) Select field 2) Type in text
32 SRS for more search options Select library tab Select resources to search Here, selected patent number
33 SRS for more search options Select library tab Select resources to search Create query
34 SRS for more search options Select library tab Select resources to search Create query Lists non-redundant nucleotide sequences from WO
35 SRS for more search options Select library tab Select resources to search Create query WO sequences
36 SRS for more search options Select library tab Select resources to search Create query WO sequences WO nucleotide sequence record in NRNL2
37 Patent sequence record in NRNL2 Patent equivalents Priority number and date Patent literature Sequence record in ENA Translation Sequence
38 SRS for more search options Select library tab Select resources to search Create query NRNL2 sequence record WO sequences
39 SRS for more search options Select library tab Select resources to search Create query WO literature WO sequences NRNL2 sequence record
40 Searching for sequence sequence search...
41 Sequence searching specialised tools Navigate to Sequence Similarity & Analysis
42 Sequence searching specialised tools Navigate to search tools
43 Sequence searching specialised tools Navigate to search tools Choose NEW INTERFACE
44 Sequence searching specialised tools Choose Search tool Navigate to search tools BLAST FASTA PSI search
45 Query length time to search When to use which search? NCBI BLAST WU-BLAST FASTA PSI-SEARCH Database size
46 When to use which search? Chose the appropriate search engine for the job (one search engine won t do everything) BLAST initial fast search FASTA better general search engine PSI-BLAST find remote family members GLSEARCH match oligo/peptide to gene/protein GGSEARCH force full length matches
47 Sequence searching specialised tools Navigate to search tools Here, try FASTA protein
48 Sequence searching specialised tools Navigate to search tools Select search tool
49 Sequence searching specialised tools Navigate to search tools Select search tool Step 1: Select database For patent proteins: Search individual patent offices or non-redundant patent datasets
50 Sequence searching specialised tools Navigate to search tools Select search tool Step 1: Select database Here, selected UniProt Knowledgebase + NR patent proteins L2
51 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database
52 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Step 2: Copy/paste sequence or upload file Copy/pasted patent protein A00210 from patent EP
53 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence
54 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Step 3: Set parameters (2) Copy/paste sequence Can change search engine
55 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Step 3: Set parameters (2) Copy/paste sequence Can change search parameters
56 How to optimise parameters? User manual provides help
57 How to optimise parameters? Choice of matrix depends on: 1. strictness of search 2. length of query sequence QUERY LENGTH MATRIX open ext >300 BLOSUM BLOSUM BLOSUM >300 PAM PAM MDM <=35 MDM <=10 MDM
58 How to optimise parameters? Choice of gap penalties depends on: 1. strictness of search larger penalty fewer gaps 2. to match scoring matrix QUERY LENGTH MATRIX open ext >300 BLOSUM BLOSUM BLOSUM >300 PAM PAM MDM <=35 MDM <=10 MDM
59 How to optimise parameters? Do I mask my sequence? Low complexity regions should be masked to avoid spurious results CA repeats poly-a tails proline-rich regions **Be careful you don t mask what you are looking for
60 How to optimise parameters? What do I use for short sequences? use strict matrices use high gap penalties avoid masking allow high e-values
61 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Step 3: Set parameters (2) Copy/paste sequence Here, use default parameters
62 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence (3) Set parameters
63 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Step 4: submit Can select to have results ed (2) Copy/paste sequence (3) Set parameters
64 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence (4) Submit (3) Set parameters
65 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Results include patent proteins (from NRPL2)... (2) Copy/paste sequence...and non-patent proteins (from UniProtKB) View additional annotation (4) Submit (non-patent proteins) (3) Set parameters
66 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence Related EMBL (4) Submit nucleotide entries (3) Set parameters
67 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence Related genomic (4) Submit information (3) Set parameters
68 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence Gene ontology (GO) (4) Submit mapping for protein (3) Set parameters
69 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence InterPro family/domain (4) Submit classification (3) Set parameters
70 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database (2) Copy/paste sequence Literature (4) Submit (3) Set parameters
71 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Functional predictions on (2) Copy/paste sequence ALL proteins (4) Submit (3) Set parameters
72 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Result summary + annotation (2) Copy/paste sequence (4) Submit (3) Set parameters
73 Sequence searching specialised tools Navigate to search tools Select search tool Functional (1) Select predictions: database InterPro family/domain classifications Extract information Visual (2) comparison Copy/paste sequence find mis- or partial matches Prioritize results Result summary + annotation (4) Submit (3) Set parameters
74 Sequence searching specialised tools Navigate to search tools Select search tool (1) Select database Functional predictions (2) Copy/paste sequence Result summary + annotation (4) Submit (3) Set parameters
75 Accessing old entries sequence archives...
76 Sequence archives ENA nucleotide sequence version archive (SVA) UniSave Search UniProt by date sequence/annotation Search by accession version archive only get specific record get all records
77 Sequence archives Provides complete version list Compare different versions View old entries
78 Sequence archives View old entries
79 Sequence archives Compare different versions
80 Summary Broad patent sequence coverage Protein/nucleotides: EPO, USTPO, JPO, KIPO Comprehensive sequence databases ENA & UniParc (PAT / PRT class data) Non-redundant patent sequences enriched Sequence archives ENA SVA & UniSave track changes Multiple search engines EB-eye text search fetch patent literature ad sequences SRS advanced text searching >100 databases (including patents) Sequence searching specialised tools; annotation-enhanced
81 User support 2Can bioinformatics user support Online help pages support
82 Any questions? Contacts: The SLING project is funded by the European Commission within Research Infrastructures of the FP7 Capacities Specific Programme, grant agreement number (Integrating Activity)
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