Copyright OpenHelix. No use or reproduction without express written consent1

NCBI RefSeq NCBI’s Reference Sequence Project Materials prepared by: Mary E. Mangan, Ph.D. Updated: Q Version 1.0

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:

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

History and Goals of RefSeq Described in 2000 Ongoing, and updated daily Copyright OpenHelix. No use or reproduction without express written consent

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

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:

RefSeq Available via NCBI RefSeq data appears in many outlets around NCBI Copyright OpenHelix. No use or reproduction without express written consent8

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

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

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

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

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:

Obtain a RefSeq Sample Record Search NCBI Entrez: clock and human Copyright OpenHelix. No use or reproduction without express written consent14

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

RefSeq mRNA Sample Overview Clock RefSeq mRNA page Copyright OpenHelix. No use or reproduction without express written consent16 { references

RefSeq Accession IDs Copyright OpenHelix. No use or reproduction without express written consent17 Basic structure: 2 letters + underscore: NM_ Various codes and keys indicate molecule types, status

RefSeq mRNA Sample Overview Clock RefSeq mRNA page Copyright OpenHelix. No use or reproduction without express written consent18 references { protein nucleotide {

Advanced Searches for RefSeq Use Entrez tools, Boolean queries, structured syntax Copyright OpenHelix. No use or reproduction without express written consent19

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:

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

RefSeqGene & Locus Reference Genomic Project RefSeqGene LRG Copyright OpenHelix. No use or reproduction without express written consent22

Related or Similar Projects VEGA vega.sanger.ac.uk CCDS Gencode Copyright OpenHelix. No use or reproduction without express written consent23

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:

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

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:

Copyright OpenHelix. No use or reproduction without express written consent27