1. Copyright OpenHelix. No use or reproduction without express written consent1

2. PROSITE PROSITE: Database of Protein Domains, Families and Functional Sites Materials prepared by: Cynthia Foote, Ph.D. www.openhelix.com Updated: Q1 2011 Version 1

3. Copyright OpenHelix. No use or reproduction without express written consent3 PROSITE Agenda Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises PROSITE: http://www.expasy.org/prosite/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Proteins from Protein Domains Families of Proteins share an overall structure Protein Domains are shared across families

5. Copyright OpenHelix. No use or reproduction without express written consent5 Database of protein domains, protein families and functional sites Presence of these domains, functional sites and protein family signatures are used to infer the function of a protein Part of Swiss-Prot collection of databases on ExPASy proteomics server PROSITE Introduction

6. Copyright OpenHelix. No use or reproduction without express written consent6 Entries and Accession Numbers ProRule Entry (PRU#) Defines a rule for identifying a Profile in a novel protein sequence PROSITE Documentation Entry (PDOC#) Essentially a domain report for a set of Matrices/Profiles and/or Patterns PROSITE Entry (PS#) Defines a Matrix/Profile PROSITE Entry (PS#) Defines a Pattern

7. Copyright OpenHelix. No use or reproduction without express written consent7 PROSITE Entry Categories Pattern - used for short well-conserved regions Matrix or Profile - uses a weighted matrix

8. Copyright OpenHelix. No use or reproduction without express written consent8 PROSITE Homepage PROSITE: http://www.expasy.org/prosite/ Access information on profiles and patterns In PROSITE PROSITE Tools Main Toolbar

9. Copyright OpenHelix. No use or reproduction without express written consent9 Credits Developed by Swiss-Prot group, led by Amos Bairoch Develops and maintains the ExPASy (Expert Protein Analysis System) proteomics server Part of Swiss Institute of Bioinformatics (SIB) in Geneva, Switzerland Funded by Swiss Federal government through the Federal Office of Education and Science, The European Commission contracts FELICS and IMPACT, and a FNS project grant Collaborations: Geneva Bioinformatics (GeneBio) SA BioAlps (Lake Geneva Biocluster) Geneva University Hospitals (HUG) University Hospital Center of Vaud (CHUV)

10. Copyright OpenHelix. No use or reproduction without express written consent10 Publications Publication and citation information: http://nar.oxfordjournals.org/cgi/reprint/gkm977v1

11. Copyright OpenHelix. No use or reproduction without express written consent11 PROSITE Agenda PROSITE: http://www.expasy.org/prosite/ Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises

12. Copyright OpenHelix. No use or reproduction without express written consent12 PROSITE Search Search by entering PROSITE Accession, or name of domain, functional site or family Search Browse PDOC50933 PROSITE: http://www.expasy.org/prosite/

13. Copyright OpenHelix. No use or reproduction without express written consent13 Search Results Description of domain, site or family Technical section PROSITE entry Click here for matrix details Domain architecture References, Copyright, Miscellaneous

14. Copyright OpenHelix. No use or reproduction without express written consent14 Domain Architecture View Proteins match CHRD profile Two domain architectures Click here to expand and see all proteins

15. Copyright OpenHelix. No use or reproduction without express written consent15 Expanded Domain Architecture View Links to all five proteins in UniProtKB/ Swiss-Prot Legend Set parameters of architecture view

16. Copyright OpenHelix. No use or reproduction without express written consent16 Technical Section Taxonomic tree view Swiss-Prot entries Retrieve alignment Retrieve list Ligand binding Sequence logo

17. Copyright OpenHelix. No use or reproduction without express written consent17 Browse PROSITE Click here

18. Copyright OpenHelix. No use or reproduction without express written consent18 Browse by Documentation Entry Click on category to narrow your search Click on accession number to bring up documentation entry Click here Click on category

19. Copyright OpenHelix. No use or reproduction without express written consent19 Browse by ProRule Description Browse by categories Browse alphabetically

20. Copyright OpenHelix. No use or reproduction without express written consent20 Browse by Taxonomic Scope Allows you to browse within a taxonomic group Also allows browsing of entries common to multiple groups or unique to a taxonomic group Groups Combination of groups

21. Copyright OpenHelix. No use or reproduction without express written consent21 Browse by Number of Hits Allows you to browse proteins associated with a PROSITE profile or pattern Click here to see list of proteins associated with PROSITE AC#

22. Copyright OpenHelix. No use or reproduction without express written consent22 PROSITE Agenda Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises PROSITE: http://www.expasy.org/prosite/

23. Copyright OpenHelix. No use or reproduction without express written consent23 ProRule Manually created rules Access from PROSITE homepage top navigation bar Provides important information about critical amino acids Increases the power of PROSITE motifs and profiles Rules are in UniRule format

24. Copyright OpenHelix. No use or reproduction without express written consent24 Search or Browse ProRule Search by entering ProRule Accession or text Browse by category SearchBrowse PRU00494 Click here

25. Copyright OpenHelix. No use or reproduction without express written consent25 ProRule Annotation General rule information Annotation Features Additional information

26. Copyright OpenHelix. No use or reproduction without express written consent26 PROSITE Agenda PROSITE: http://www.expasy.org/PROSITE/ Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises

27. Copyright OpenHelix. No use or reproduction without express written consent27 ScanProsite Scan a sequence against patterns and profiles in database Quick scan Advanced scan PROSITE: http://www.expasy.org/prosite/

28. Copyright OpenHelix. No use or reproduction without express written consent28 Quick Scan Enter sequence, UniProtKB ID or Accession in text box Enter maximum of 8 sequences to scan Enter sequence or accession here Uncheck to include

29. Copyright OpenHelix. No use or reproduction without express written consent29 Advanced Scan Selections Enter sequence or accession Here Enter PROSITE accession or your own pattern here Click here

30. Copyright OpenHelix. No use or reproduction without express written consent30 Advanced Scan P29279 PS50092 PS00222 Click here

31. Copyright OpenHelix. No use or reproduction without express written consent31 PROSITE Scan Results Two hits Profiles Patterns Location Absent Consensus pattern

32. Copyright OpenHelix. No use or reproduction without express written consent32 PROSITE Agenda Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises PROSITE : http://www.expasy.org/prosite/

33. Copyright OpenHelix. No use or reproduction without express written consent33 PRATT Tool that allows user to find conserved patterns from a group of unaligned protein sequences Click here PROSITE: http://www.expasy.org/prosite/

34. Copyright OpenHelix. No use or reproduction without express written consent34 PRATT Homepage Input sequences in FASTA file or Swiss-Prot format To modify parameters, go to EBI PRATT server for advanced tool Input sequences or multiple alignment of sequences Advanced tool

35. Copyright OpenHelix. No use or reproduction without express written consent35 PRATT Pattern Search FASTA file of mouse and rat GDNF family receptor alpha-1 sequences Click here Uncheck

36. Copyright OpenHelix. No use or reproduction without express written consent36 PRATT Results Displays amino acids in conserved pattern

37. Copyright OpenHelix. No use or reproduction without express written consent37 PROSITE Agenda PROSITE: http://www.expasy.org/PROSITE/ Introduction and Credits PROSITE Search ProRule ScanProSite PRATT MyDomains Summary Exercises

38. Copyright OpenHelix. No use or reproduction without express written consent38 MyDomains Tool which allows user to create custom domain figures Click here PROSITE: http://www.expasy.org/prosite/

39. Copyright OpenHelix. No use or reproduction without express written consent39 MyDomains Homepage Input length and scale Domains Your Figure

40. Copyright OpenHelix. No use or reproduction without express written consent40 PROSITE Agenda PROSITE: http://www.expasy.org/prosite/ Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises

41. Copyright OpenHelix. No use or reproduction without express written consent41 Summary PROSITE: http://www.expasy.org/prosite/ PROSITE describes protein domains, families and functional sites Data can help you understand protein function

42. Copyright OpenHelix. No use or reproduction without express written consent42 Detailed Results PROSITE results can help to answer your research questions!

43. Copyright OpenHelix. No use or reproduction without express written consent43 Many Tools Available Scan your sequences against PROSITE with ScanProsite Create beautiful custom domain graphics with MyDomains Find a common pattern between sequences using PRATT

44. Copyright OpenHelix. No use or reproduction without express written consent44 PROSITE Agenda PROSITE: http://www.expasy.org/prosite/ Introduction and Credits PROSITE Search ProRule ScanProsite PRATT MyDomains Summary Exercises

45. Copyright OpenHelix. No use or reproduction without express written consent45