1. Advanced SRS Course 12/12/02 -Linking -Subentries -Applications

2. Linking in SRS

3. Types of Links Hyperlinks -links between entries which are displayed as hypertext -useful for examining entries that are referenced directly from entries Query links -allow you to construct queries using the relationships between databanks -require SRS to search through entries or indices in other databanks looking for matches

4. Links between Databases SWISS-PROT EMBL PDB InterPro PROSITE PFAM BLOCKS

5. Advantages of SRS Linking Links are bi-directional ABC Direct link from ‘A’ to ‘B’Direct link from ‘B’ to ‘C’ Multistep link from ‘A’ to ‘C’

6. Database Network Graph

7. The link page Two forms of the link page: -type you see if you initiate linking from either the query manager or the query result page -type you see if you initiate linking from an individual entry page The difference is at the top of these pages – one provides a “find all entries” option, the other does not (see next 2 slides)

8. From query manager or query result page

9. Find all entries options In the selected databanks which are linked to the current query - this returns entries from other databanks which have links with entries in the current query In the current query which are linked to all selected databanks - this limits the query so that it includes only the entries(from the original query) which are linked to all of the selected databanks In the current query which are not linked to any of the selected databanks - this limits the query so that it includes only the entries(from the original query) which do not have links to the specified databanks

10. From an individual entry page No ‘find all entries’ options available

11. Linking from query manager page Can link from a single query or from multiple queries two ways to link your queries from the query manager page: - tick the checkbox that corresponds to a query set and click the LINK button - use the text box beside the Expression button

12. Expression linking Useful alternative to using the linking pages Can be used to search for a link between two or more sets of results or between a set of results and a databank

13. Linking operators < entries in the set or databank to the left of the operator are returned if they have a link to any entries in the set or databank to the right of the operator > entries in the set or databank to the right of the operator are returned if they have a link to any entries in the set or databank to the left of the operator

14. Linking operations <Q1 < Q2In Q1 that link to Q2 >Q1 > Q2In Q2 that link to Q1 combined with logical operators: < &Q1<Q2 & Q3In Q1 that link to Q2 &Q3 < |Q1<Q2 | Q3In Q1 that link to Q2 or Q3 < !Q1<Q2 ! Q3In Q1 that link to Q2 but not Q3

15. A1 A2 A3 A4 A5 A6 B1 B2 B3 B4 B5 A B A > B is B2 B3 B4 (all entries in B that have links to A) A < B is A1 A2 A5 A6 (all entries in A that have links to B)

16. Subentries

17. Necessary when there is repeated structured information within an entry FT DOMAIN 1 12 LUMENAL (POTENTIAL).DOMAIN FT TRANSMEM 13 33 POTENTIAL.TRANSMEM FT DOMAIN 34 55 CYTOPLASMIC (POTENTIAL).DOMAIN FT TRANSMEM 56 76 POTENTIAL.TRANSMEM FT DOMAIN 77 95 LUMENAL (POTENTIAL).DOMAIN DR EMBL; L44581; AAA99933.1; -.L44581AAA99933 DR EMBL; L44582; AAA99934.1; -.L44582AAA99934 DR EMBL; L44583; AAA99935.1; -.L44583AAA99935 DR EMBL; L44584; AAA99936.1; -.L44584AAA99936 DR EMBL; L44585; AAA99937.1; -.L44585AAA99937 …..

18. Use subentries to: Search for entries containing one or more subentries with certain values and obtain a list of entry references Search for subentries with certain values and obtain a list of subentry references

19. Subentries have a double function: They are part of the entry and often require data from other fields in order for their meaning to be resolved and displayed Example: a SWISS-PROT feature requires part of the entry’s sequence to be displayed They can be regarded as databanks themselves and can be indexed and queried independently from the entries Example: search all the transmembrane segments with a given range of length

20. Subentries available Protein databases have 5 subentries: –Reference –Comment –Links –Feature –Counter Nucleotide databases have 3 subentries: –Reference –Features –Counters

21. Controlled vocabularies Some of the fields belonging to the subentries have a predetermined number of keys ( as specified by the database documentation). These fields have a controlled vocabulary and when you use the extended query forms you can select a value from a drop down menu. Examples are: –CommentType –DbName –FtKey –CountItem

22. The Counter subentry This is a special subentry created by SRS on the fly. It counts the number of times particular feature keys, comment types and links to a certain database occur within an entry It can be used to answer questions like: –How many entries have 3 or more links to EMBL? –How many entries have more than 8 disulphide bridges? –How many entries have 2 or more comments about function?

23. Subentry fields In the standard query form each subentry field name is preceded by the name of the subentry to which it belongs: Reference:authors Feature:FtKey Links:DbName The extended query form is divided up into sections. The top section contains the fields belonging to entry and below this are the subentries and the fields that they contain

24. Links with sets containing subentries Two types: –Simple Links –Parent Links

25. It is not possible to combine sets of entries with sets of subentries using the logical operators but link operators may be used between sets of entries and sets of subentries [swissprot-org:human] > [swissprot-ftkey:transmem] gives a set of transmembrane segment subentries found in human proteins [swissprot-org:human] < [swissprot-ftkey:transmem] returns all human entries that have a transmembrane segment Simple links

26. Parent Links Sometimes it is necessary to do an explicit conversion from subentries to entries. This can be done using the operand parent. This method looks for links from the subentries to their respective parent entries and retrieves a set containing parent entries. [swissprot-ftkey:transmem] > parent gives the parent entries for the set of subentries from SWISS-PROT that have transmembrane sequence features Logical operators can then be used to combine the set of parent entries with another set of entries

27. Types of entries Query Form

28. Using entry….. Feature that is 10 aa in length

29. Using feature….. Only returns transmem regions of exactly 10 aa

30. Applications

31. Applications in SRS SWISSPROT Upload user owned data Sequence query Run BLAST launch BLAST results - text file BLAST Indexing linking Pathway Prosite

32. Protein Applications in SRS Homology and similarity tools: BLASTP : database search tool FASTA : database search tool MPSrch Protein function analysis tools: PPSearh : BLASTProdom ScanRegExp FingerPrintScan PfScan InterProScan MPSrch Sequence analysis tools: - ClustalW

33. Nucleotide applications in SRS Homology and similarity tools BLASTN NFASTA FASTX FASTY Sequence analysis tools: NClustalW RestrictionMap