1. ©CMBI 2007 Search tools Google, MRS, (SRS)

2. ©CMBI 2007 Search tools Google= Thé best generic search and retrieval system MRS= Maarten’s Retrieval System MRS is the Google of the biological database world SRS= Sequence 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 2007 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 2007 MRS

5. ©CMBI 2007 SRS 7.1

6. ©CMBI 2007 The main MRS search window provides three options: Select databases Enter keywords Appends wildcards to keywords MRS Main Search Window

7. ©CMBI 2007 MRS Database Selection You can choose between selecting all databases or just one of them. Don't worry about selecting all databases at the same time, MRS is fast enough.

8. ©CMBI 2007 MRS Search options Simply type your keywords in the keyword field You can use wildcards (*) But think about your query first!!

9. ©CMBI 2007 MRS Search options (2) If you know the fields of the database you are searching in you can specify your query further But think about your query first!!

10. ©CMBI 2007 Combine in MRS AND (implicit) OR NOT

11. ©CMBI 2007 Submit / Search Enter your question and............SUBMIT/SEARCH! MRS/SRS creates a result, or a “query set”, or “hitlist”. With the result you can do different things in MRS: –View the hits –Blast single hit sequences –Clustal multiple hit sequences

12. ©CMBI 2007 MRS - View Hits

13. ©CMBI 2007 MRS - Facilities Home brings you back to the start page of MRS. That is the page from which you can do keyword searches. Blast brings you to the MRS-page from which you can do Blast searches. Blast results brings you to the page where MRS stores your Blast results. Clustal brings you to the MRS-page from which you can do Clustal alignments. Databanks lists all databases that MRS can search in. DB:uniprot lists the currently selected database.

14. ©CMBI 2007 Summary MRS vs SRS 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’. 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.

15. ©CMBI 2007 Try it yourself with the exercises http://mrs.cmbi.ru.nl/ http://srs.bioinformatics.nl/

16. ©CMBI 2007 SRS - 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.

17. ©CMBI 2007 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

18. ©CMBI 2007 SRS Standard Query Form

19. ©CMBI 2007 SRS Hits

20. ©CMBI 2007 Display options

21. ©CMBI 2007 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.

22. ©CMBI 2007 View option “proteinChart” in SRS

23. ©CMBI 2007 Results

24. ©CMBI 2007 Combine in SRS