1. ©CMBI 2005 Search tools Google, MRS, SRS

2. ©CMBI 2004 Search tools SRS = Sequence Retrieval System MRS = Maarten’s Retrieval System Google = Thé best generic search and retrieval system Google searches everywhere for everything SRS and MRS search in selected data environments As SRS and MRS know the format, lay-out, and data- type of the databases you want to query, they can search much more selective than Google. Most search principles, however, are the same between these systems.

3. ©CMBI 2004 MRS / SRS Indexing and retrieval system for databases Mainly used for (but not restricted to) protein/nucleic acid and related databases –DNA and protein sequences –Sequence related information (e.g. alignments, protein, domains, enzymes, metabolic pathways, structural information) –Genomic information –Hereditary information

4. ©CMBI 2004 SRS 7.1

5. ©CMBI 2004 MRS

6. ©CMBI 2004 Start directly with “Quick Search” Or ‘something similar’. This is Google-like. Most search engines also provide more extended searches. In MRS quick-search is the default.

7. ©CMBI 2004 Or ‘something similar’. This is Google-like. Most search engines also provide more extended searches. In MRS quick-search is the default. MRS always starts with ‘Quick Search’

8. ©CMBI 2004 MRS / SRS Search options Quick Search: quick and ‘dirty’ (Google raw) SRS uses pre-selected database MRS uses all databases (fast enough) OR: select database(s) of choice use standard or extended query form in SRS use selected or all databases in MRS use special commands in MRS when you know the fields in the database

9. ©CMBI 2004 SRS Standard Query Form

10. ©CMBI 2004 Submit / Search Enter your question and............SUBMIT/SEARCH! MRS/SRS creates a result, or a “query set”, or “hits”. With the result you can do different things in SRS: –view with different display options –combine with other results With the result you can do different things in MRS: –Blast single hit sequences –Clustal multiple hit sequences

11. ©CMBI 2004 SRS Hits

12. ©CMBI 2004 MRS Hits

13. ©CMBI 2004 Display options

14. ©CMBI 2004 Display options in SRS Common options: * Names only * * Complete entries * In case of SwissProt: SwissView proteinChart User defined options: You can ‘Create a view’ in the standard or extended query form. These display options are named after the database.

15. ©CMBI 2004 View option “proteinChart” in SRS

16. ©CMBI 2004 Results

17. ©CMBI 2004 Results in SRS Each query list is stored* in the results section You can always* view your previous query results You can link query results to databases You can also combine query results *) During one SRS session

18. ©CMBI 2004 Combine in SRS/MRS AND OR BUTNOT

19. ©CMBI 2004 Combine in SRS

20. ©CMBI 2004 Summary SRS vs MRS Nine out of ten times MRS beats SRS because of speed. Occasionally, there are things only SRS can do. MRS is in-house, so its performance is ‘predictable’. The firm that made SRS recently file for chapter 11. These search engines can do things for you like hyper-linking to other databases or information systems, launching other software (BLAST, Clustal, etc). There is no bioinformatics without Google and SRS or MRS.

21. ©CMBI 2004 Try it yourself with the exercices http://srs.bioinformatics.nl/ http://mrs.cmbi.ru.nl/