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

2. NCBI RefSeq NCBI’s Reference Sequence Project Materials prepared by: Mary E. Mangan, Ph.D. www.openhelix.com Updated: Q1 2011 Version 1.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 NCBI RefSeq Introduction and Credits Finding RefSeq Data Understanding the Records Beyond RefSeq Summary Exercises RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq

4. Sequence Data Repositories Need to identify and collect sequences RefSeq project provides a collected and curated set Derived from GenBank, but not the same as primary archival sequences Copyright OpenHelix. No use or reproduction without express written consent4 www.ncbi.nlm.nih.gov/genbank

5. History and Goals of RefSeq www.ncbi.nlm.nih.gov/RefSeq Described in 2000 Ongoing, and updated daily Copyright OpenHelix. No use or reproduction without express written consent5 www.ncbi.nlm.nih.gov/pubmed/10592200 www.ncbi.nlm.nih.gov/pubmed/ 21097890

6. RefSeq Process NCBI Handbook for process details RefSeq records assembled and maintained Updates may occur and are indicated on records Copyright OpenHelix. No use or reproduction without express written consent6 “Sequences enter the RefSeq curation process flow by a combination of computational analysis, collaboration, and in- house curation” status

7. Copyright OpenHelix. No use or reproduction without express written consent7 NCBI RefSeq Introduction and Credits Finding RefSeq Data Understanding the Records Beyond RefSeq Summary Exercises RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq

8. RefSeq Available via NCBI www.ncbi.nlm.nih.gov RefSeq data appears in many outlets around NCBI Copyright OpenHelix. No use or reproduction without express written consent8

9. RefSeq from the Project Page RefSeq project page as entry point Entrez Search of all databases Or choose specific topic Copyright OpenHelix. No use or reproduction without express written consent9 www.ncbi.nlm.nih.gov/RefSeq

10. RefSeq via PubMed PubMed www.pubmed.gov BRCA1 search, explore Gene links Copyright OpenHelix. No use or reproduction without express written consent10

11. RefSeq via BLAST BLAST blast.ncbi.nlm.nih.gov Find RefSeq records with a sequence search Copyright OpenHelix. No use or reproduction without express written consent11 RefSeq

12. RefSeq via FTP FTP downloads of bulk data Can use RefSeq in your projects and analyses Copyright OpenHelix. No use or reproduction without express written consent12 www.ncbi.nlm.nih.gov/RefSeq

13. Copyright OpenHelix. No use or reproduction without express written consent13 NCBI RefSeq Introduction and Credits Finding RefSeq Data Understanding the Records Beyond RefSeq Summary Exercises RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq

14. Obtain a RefSeq Sample Record www.ncbi.nlm.nih.gov Search NCBI Entrez: clock and human Copyright OpenHelix. No use or reproduction without express written consent14

15. RefSeq via Gene Page Clock, human record Access RefSeq details from Gene Record Copyright OpenHelix. No use or reproduction without express written consent15

16. RefSeq mRNA Sample Overview Clock RefSeq mRNA page www.ncbi.nlm.nih.gov/nuccore/25777594 Copyright OpenHelix. No use or reproduction without express written consent16 { references

17. RefSeq Accession IDs Copyright OpenHelix. No use or reproduction without express written consent17 www.ncbi.nlm.nih.gov/RefSeq/key.html Basic structure: 2 letters + underscore: NM_0000000 Various codes and keys indicate molecule types, status

18. RefSeq mRNA Sample Overview Clock RefSeq mRNA page www.ncbi.nlm.nih.gov/nuccore/25777594 Copyright OpenHelix. No use or reproduction without express written consent18 references { protein nucleotide {

19. Advanced Searches for RefSeq www.ncbi.nlm.nih.gov/RefSeq/key.html Use Entrez tools, Boolean queries, structured syntax Copyright OpenHelix. No use or reproduction without express written consent19

20. Copyright OpenHelix. No use or reproduction without express written consent20 NCBI RefSeq Introduction and Credits Finding RefSeq Data Understanding the Records Beyond RefSeq Summary Exercises RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq

21. RefSeq Data in Other Projects Map Viewer UCSC Genome Browser MGI GBrowse Mouse RefSeq Reactome Copyright OpenHelix. No use or reproduction without express written consent21

22. RefSeqGene & Locus Reference Genomic Project RefSeqGene www.ncbi.nlm.nih.gov/refseq/rsg LRG www.lrg-sequence.org Copyright OpenHelix. No use or reproduction without express written consent22 www.ncbi.nlm.nih.gov/pubmed/18927115 www.ncbi.nlm.nih.gov/pubmed/20398331

23. Related or Similar Projects VEGA vega.sanger.ac.uk CCDS www.ncbi.nlm.nih.gov/projects/CCDS Gencode www.gencodegenes.org Copyright OpenHelix. No use or reproduction without express written consent23

24. Copyright OpenHelix. No use or reproduction without express written consent24 NCBI RefSeq Introduction and Credits Finding RefSeq Data Understanding the Records Beyond RefSeq Summary Exercises RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq

25. NCBI RefSeq Summary RefSeq from NCBI Accessible from many NCBI tools Accessible from other projects Evolves and expands Copyright OpenHelix. No use or reproduction without express written consent25

26. Copyright OpenHelix. No use or reproduction without express written consent26 NCBI RefSeq Introduction and Credits Finding RefSeq Data Understanding the Records Beyond RefSeq Summary Exercises RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq

27. Copyright OpenHelix. No use or reproduction without express written consent27