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

2. Entrez Protein NCBI’s Protein Database Materials prepared by: Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q2 2012 Version 4.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 NCBI Protein Agenda Introduction and Credits Basic Searches “My NCBI” Advanced Searches Summary Exercises http://www.ncbi.nlm.nih.gov/protein

4. Copyright OpenHelix. No use or reproduction without express written consent4 An Introduction to Entrez Protein Imported from several sources & updated daily Help, FAQs, links to explore Many Entrez tools available http://www.ncbi.nlm.nih.gov/protein

5. Copyright OpenHelix. No use or reproduction without express written consent5 Protein Entries - Extensive Details & Options More options BLink - BLAST Link: Pre-computed BLAST results

6. http://www.ncbi.nlm.nih.gov/protein Copyright OpenHelix. No use or reproduction without express written consent6 Entrez Provides Lots of Help An entire book of help is available on-line. Chapters on searching, displaying, saving data and more!

7. Copyright OpenHelix. No use or reproduction without express written consent7 Additional Homepage Resources Getting Started Contact NCBI Resources

8. Copyright OpenHelix. No use or reproduction without express written consent8 NCBI Homepage - The Interlinked Entrez Network http://www.ncbi.nlm.nih.gov Protein All

9. Copyright OpenHelix. No use or reproduction without express written consent9 Entrez Global Query Results Global query -many results in many fields Literature, SNPs, nucleotide, protein, probe, 3D, domain, chemical, MeSH terms & more Entrez Protein entries linked In addition, Entrez Protein has thousands of matches Global Entrez query for insulin

10. Copyright OpenHelix. No use or reproduction without express written consent10 Nucleic Acids Research Reference: http://nar.oxfordjournals.org/content/40/D1/D13

11. Copyright OpenHelix. No use or reproduction without express written consent11 NCBI Protein Agenda Introduction and Credits Basic Searches “My NCBI” Advanced Searches Summary Exercises http://www.ncbi.nlm.nih.gov/protein

12. Copyright OpenHelix. No use or reproduction without express written consent12 Beginning A Basic Search at Entrez Protein You can begin to search at Entrez Protein homepage To Access Entrez Protein from NCBI homepage, select “Protein” from menu & click “Search” NCBI Homepage: http://www.ncbi.nlm.nih.gov/

13. http://www.ncbi.nlm.nih.gov/protein Copyright OpenHelix. No use or reproduction without express written consent13 A Basic Search From Entrez Protein Homepage Many links available, including Help, FAQs, Tools & other protein resources Enter Tau & click on “Search” to submit your query Tau

14. Copyright OpenHelix. No use or reproduction without express written consent14 Basic Search Results - 1 Basic Entrez options “Send to” File, “My NCBI” Collections, or your Clipboard, for saving, printing & storing Check box Display records in different formats Choose how many items per page Sort results by different variables

15. Copyright OpenHelix. No use or reproduction without express written consent15 Basic Search Results - 2 Click to access record Links to GenPept, FASTA, Graphics, Related Sequences & Identical Proteins

16. Copyright OpenHelix. No use or reproduction without express written consent16 Basic Search Results - 3 Filters - click to view that subset & manage via “My NCBI” Manage Filters Results categorized by taxonomy, select “More” to expand, view “List”, or “Tree”

17. Copyright OpenHelix. No use or reproduction without express written consent17 Basic Search Results - 4 Search details Find related data Scroll down to Recent activity

18. Copyright OpenHelix. No use or reproduction without express written consent18 Entrez Protein Record Overview Protein records provide many details Let’s take a closer look at a protein record Click to access record Content & size of records can vary greatly between entries Organization of records: General Annotation; Comments; Features; Sequence

19. Copyright OpenHelix. No use or reproduction without express written consent19 Entrez Protein Record - Options at the Top

20. Copyright OpenHelix. No use or reproduction without express written consent20 The Top Section of a Protein Record - 1 Database source, version & accession number, cross- references Accession number Skip to that section General information, dates, definition

21. Copyright OpenHelix. No use or reproduction without express written consent21 Side Options Analyze sequence Articles Homologs External links Internal links Recent activity Identical proteins Pathways RefSeq info Gene info

22. Copyright OpenHelix. No use or reproduction without express written consent22 The Top Section of A Protein Record - 2 References with links to PubMed, note the remark here Source, brief lineage, link

23. Copyright OpenHelix. No use or reproduction without express written consent23 The Comment Section of A Protein Record Function Subunit Subcellular Location Alternative Products Interaction

24. Copyright OpenHelix. No use or reproduction without express written consent24 The Features Section of A Protein Record Source, gene & protein info, also details on specific domains with links Region of interest

25. Copyright OpenHelix. No use or reproduction without express written consent25 The Sequence Section of A Protein Record The last section of the protein record contains the amino acid sequence of your protein Note: content of sections may vary, but overall order maintained

26. Copyright OpenHelix. No use or reproduction without express written consent26 NCBI Protein Agenda Introduction and Credits Basic Searches “My NCBI” Advanced Searches Summary Exercises http://www.ncbi.nlm.nih.gov/protein

27. Copyright OpenHelix. No use or reproduction without express written consent27 username My NCBI: Sign In or Register password

28. Copyright OpenHelix. No use or reproduction without express written consent28 My NCBI includes:  Search databases  My Bibliography  Recent Activity  Save Searches  Collections  Filters  Customization options My NCBI

29. Copyright OpenHelix. No use or reproduction without express written consent29 Customization Basic search My Bibliography Recent Activity Collections Saved Searches Filters NCBI Search http://www.ncbi.nlm.nih.gov/myncbi/manageportlets/ BLAST

30. Copyright OpenHelix. No use or reproduction without express written consent30 Bibliography Build bibliography from PubMed results Bibliography help: http://www.ncbi.nlm.nih.gov/books/NBK53595/

31. Copyright OpenHelix. No use or reproduction without express written consent31 Saved Searches BioSystem saved searches Protein saved searches

32. Copyright OpenHelix. No use or reproduction without express written consent32 Collections Collections include:  My Bibliography  Favorites  Other Citations  User-created Collections Permanent collections, by default Created collections, “Send to” option

33. Copyright OpenHelix. No use or reproduction without express written consent33 Filters Basic Protein Filters

34. Change DB to Protein Copyright OpenHelix. No use or reproduction without express written consent34 Filter Management My NCBI: Adding Power to Your NCBI Gene Searches Molecular DB Database Taxonomy Other database TP53 Counts

35. Copyright OpenHelix. No use or reproduction without express written consent35 NCBI Protein Agenda Introduction and Credits Basic Searches “My NCBI” Advanced Searches Summary Exercises http://www.ncbi.nlm.nih.gov/protein

36. Copyright OpenHelix. No use or reproduction without express written consent36 Tips for Advanced Searches Many useful tips in Entrez book in Help menu at URL below Use Limits, Index, History, field qualifiers Boolean Operators: AND, NOT, OR, must be capitalized Author search format: Cohen JK Use quotes for a phrase (otherwise AND will be assumed) Wild-card by * (asterisk), for ex: musc* finds muscle, musculature, but also muscarinic Entrez Help: http://1.usa.gov/R796qY

37. Too many results Click Limits Copyright OpenHelix. No use or reproduction without express written consent37 Advanced Search - Limits Dates Fields Source Exclude Modified date Gene Location Click Search Our Example: published in last 3 years, Tau in title Segmented Sequences

38. Copyright OpenHelix. No use or reproduction without express written consent38 Results of Limited Query Check your Search details “Change” - back to Limits form “Remove” - removes Limits Click

39. Copyright OpenHelix. No use or reproduction without express written consent39 Advanced Search Builder Help click

40. Search term click Copyright OpenHelix. No use or reproduction without express written consent40 microtubule-associated protein Advanced Search Builder, cont. Search term

41. Copyright OpenHelix. No use or reproduction without express written consent41 Search Builder Results

42. Copyright OpenHelix. No use or reproduction without express written consent42 NCBI Protein Agenda Introduction and Credits Basic Searches “My NCBI” Advanced Searches Summary Exercises http://www.ncbi.nlm.nih.gov/protein

43. Copyright OpenHelix. No use or reproduction without express written consent43 Summary http://www.ncbi.nlm.nih.gov/protein Detailed annotation

44. Copyright OpenHelix. No use or reproduction without express written consent44 Many Helpful Tools & Options Basic & Advanced searches are easy Customize your searches

45. Copyright OpenHelix. No use or reproduction without express written consent45 NCBI Protein Agenda Introduction and Credits Basic Searches “My NCBI” Advanced Searches Summary Exercises http://www.ncbi.nlm.nih.gov/protein

46. Copyright OpenHelix. No use or reproduction without express written consent46