1. A Field Guide to GenBank and NCBI Molecular Biology Resources
slightly modified from
Peter Cooper
ftp://ftp.ncbi.nih.gov/pub/cooper/FieldGuide/
Eric Sayers
ftp://ftp.ncbi.nih.gov/pub/sayers/Field_Guide/U_Penn/

2. NCBI Resources About NCBI NCBI Sequence Databases
Primary Database – GenBank
Derivative Databases - RefSeq
Entrez Databases and Text Searching
BLAST Services
Genomic Resources

3. The National Center for Biotechnology Information (NCBI)
Created as a part of NLM in 1988
Establish public databases
Perform research in computational biology
Develop software tools for sequence analysis
Disseminate biomedical information
Tools: BLAST(1990), Entrez (1992)
GenBank (1992)
Free MEDLINE (PubMed, 1997)
Human genome (2001)

4. NCBI Home Page http://www.ncbi.nlm.nih.gov
To learn more, visit the
“Site Map” and
“About NCBI”
web pages

5. About NCBI

6. Some NCBI Statistics….

7. Users per day
Christmas Day

8. Molecular Databases Primary Databases Derivative Databases
Original submissions by experimentalists
Database staff organize but don’t add additional information
Example: GenBank
Derivative Databases
Human curated
compilation and correction of data
Example: SWISS-PROT, NCBI RefSeq mRNA
Computationally Derived
Example: UniGene
Combinations
Example: NCBI Genome Assembly

9. What is GenBank? NCBI’s Primary Sequence Database
Nucleotide only sequence database
GenBank Data
Direct submissions individual records (BankIt, Sequin)
Batch submissions via (EST, GSS, STS)
ftp accounts established for sequencing centers
Data shared amongst three collaborating databases:
GenBank
DNA Database of Japan (DDBJ).
European Molecular Biology Laboratory Database
(EMBL)

10. NIH NIG EMBL The International Nucleotide Sequence
Database Collaboration
NIH
Entrez
Sequin
BankIt
ftp
NCBI
GenBank
Submissions
Updates
Submissions
Updates
EMBL
DDBJ
EBI
CIB
NIG
Submissions
Updates
SRS
EMBL
getentry

11. GenBank: NCBI’s Primary Sequence Database
full release every two months
incremental and cumulative updates daily
available only through internet
ftp://ftp.ncbi.nih.gov/genbank/
Release 133 December 2002
22,318,883 Records
28,507,990,166 Nucleotides
110,000 + Species
>90 Gigabytes of data

12. Entrez Nucleotide RefSeq 1% EMBL 9% DDBJ 19% GenBank 71%
23,464,770 records

13. Primary vs. Derivative Databases
ACGTGC
Curators C GA
ATT GA C GA C
ATT GA C
RefSeq
TATAGCCG
Sequencing
Centers
ACGTGC
TATAGCCG
AGCTCCGATA
CCGATGACAA
ATTGACTA
CGTGA
TTGACA
Labs
TTGACA
ACGTGC
TTGACA
Genome
Assembly
TATAGCCG
CGTGA
ATTGACTA
ACGTGC
TATAGCCG
CGTGA
CGTGA
TATAGCCG
ATTGACTA
ATTGACTA
ATTGACTA
ATTGACTA
TATAGCCG
TTGACA
TATAGCCG
TATAGCCG
TATAGCCG
TATAGCCG
ATT C
GenBank GA
UniGene AT C C
ATT C
Algorithms
ATT GA
ATT GA GA
ATT GA C GA
ATT GA C GA C
ATT GA C C

14. Traditional GenBank Divisions
Direct Submissions (Sequin and BankIt)
Accurate
Well characterized
BCT Bacterial and Archeal
INV Invertebrate
MAM Mammalian (ex. ROD and PRI)
PHG Phage
PLN Plant and Fungal
PRI Primate
ROD Rodent
SYN Synthetic (cloning vectors)
VRL Viral
VRT Other Vertebrate

15. A Traditional GenBank Record
Locus Field
Molecule Type
Modification Date
GenBank Division
Definition Line
Accession Number
Version
GI (GenInfo)
Keywords
Taxonomy

16. A Traditional GenBank Record

17. Bulk Sequence Divisions of GenBank
Batch Submissions ( and ftp)
Inaccurate
Poorly Characterized
EST Expressed Sequence Tag
STS Sequence Tagged Site
GSS Genome Survey Sequence
HTG High Throughput Genomic
HTC High Throughput cDNA

18. Organization of GenBank
11 Traditional Divisions
PAT 4%
Traditional 8%
1 Patent Division
STS, HTG, HTC 2%
GSS 19%
EST 67%
5 Bulk Divisions
23,087,196 records

19. What is UniGene? A gene-oriented view of sequence entries
MegaBlast-based automated sequence clustering
Nonredundant set of gene-oriented clusters
Each cluster represents a unique gene
Provides information on tissue-specific expression and map locations
Includes well-characterized genes and novel ESTs
Useful for gene discovery and selection of mapping reagents

20. Organisms Represented in UniGene

21. Genome Sequencing Whole BAC insert (or genome)
shredding
sequencing
cloning isolating
GSS division
or trace archive
assembly
Draft Sequence (HTG division)

22. Working Draft Sequence
gaps

23. HTG Division: High Throughput Genome
phase 1
phase 2
phase 3
ROD
Acc = AC
Acc =AC
Acc = AC
HTG

24. HTG Division: High Throughput Genome

25. NCBI’s Third Party Annotation (TPA) Database
NEW
NCBI now accepts the submission of new annotations of existing GenBank sequences;
Facilitates the annotation of genomes by experts;

26. A Sample TPA record

27. RefSeq: NCBI’s Derivative Sequence Database
Curated transcripts and proteins
reviewed
human, mouse, rat, fruit fly, zebrafish, arabidopsis
Human model transcripts and proteins
Assembled Genomic Regions (contigs)
draft human genome
mouse genome
Chromosome records
Microbial
viral
organelle

28. The RefSeq Accession Numbers
mRNAs and Proteins
NM_ Curated mRNA
NP_ Curated Protein
NR_ Curated non-coding RNA
XM_ Predicted Transcript (human, mouse)
XP_ Predicted Protein (human, mouse)
XR_ Predicted non-coding RNA
Gene Records
NG_ Reference Genomic Sequence (human)
Assemblies
NT_ Contig (Mouse and Human)
NW_ Supercontig (Mouse)
NC_ Chromosome (Microbial,Viral,Arabidopsis )
NR_ Interim Identifier for Microbial Chromosomes
human
mouse
rat
fruit fly
zebrafish
Arabidopsis

29. Curated RefSeq Records: NM_, NP_

30. Entrez: Linking and Neighboring

31. The Entrez Databases

32. The (ever) Expanding Entrez System
Journals
UniGene
Books
SNP
PubMed
PubMed
Central
UniSTS
Nucleotide
PopSet
Protein
Entrez
ProbeSet
Genome
Structure
Taxonomy
CDD
3D Domains
OMIM

33. glucose 6 phosphate dehydrogenase
Entrez Nucleotides
glucose 6 phosphate dehydrogenase

34. Document Summaries:
glucose 6 phosphate dehydrogenase[All Fields] = 748 hits

35. Entrez Nucleotides: Limits
Accession
All Fields
Author Name
EC/RN Number
Feature key
Filter
Gene Name
Issue
Journal Name
Keyword
Modification Date
Organism
Page Number
Primary Accession
Properties
Protein Name
Publication Date
SeqID String
Sequence Length
Substance Name
Text Word
Title Word
Uid
Volume
glucose 6 phosphate dehydrogenase

36. Entrez Nucleotides: Preview/Index

37. Adding Terms: Preview/Index
Accession
All Fields
Author Name
EC/RN Number
Feature key
Filter
Gene Name
Issue
Journal Name
Keyword
Modification Date
Organism
Page Number
Primary Accession
Properties
Protein Name
Publication Date
SeqID String
Sequence Length
. . .

38. Plant G6PD mRNAs

39. Display: Formats, Links, and Neighbors
Summary
Brief
ASN.1
FASTA
XML
GenBank
GI list
LinkOut
Nucleotide Neighbors
Genome Links
ProbeSet Links
OMIM Links
PopSet Links
Protein Links
PubMed Links
SNP Links
Structure Links
Taxonomy Links
UniSTS Links

40. FASTA definition line >gi|603218|gb|U18238.1|MSU18238 >
>gi|603218|gb|U |MSU18238 Medicago sativa glucose-6-phosphate dehyd
CCACCAGATATAATTAAGTAGATCAGAGTAGAAGAAGATGGGAACAAATGAATGGCATGTAGAAAGAAGA
GATAGCATAGGTACTGAATCTCCTGTAGCAAGAGAGGTACTTGAAACTGGCACACTCTCTATTGTTGTGC
TTGGTGCTTCTGGTGATCTTGCCAAGAAGAAGACTTTTCCTGCACTTTTTCACTTATATAAACAGGAATT
GTTGCCACCTGATGAAGTTCACATTTTTGGCTATGCAAGGTCAAAGATCTCCGATGATGAATTGAGAAAC
AAATTGCGTAGCTATCTTGTTCCAGAGAAAGGTGCTTCTCCTAAACAGTTAGATGATGTATCAAAGTTTT
TACAATTGGTTAAATATGTAAGTGGCCCTTATGATTCTGAAGATGGATTTCGCTTGTTGGATAAAGAGAT
TTCAGAGCATGAATATTTGAAAAATAGTAAAGAGGGTTCATCTCGGAGGCTTTTCTATCTTGCACTTCCT
CCTTCAGTGTATCCATCCGTTTGCAAGATGATCAAAACTTGTTGCATGAATAAATCTGATCTTGGTGGAT
GGACACGCGTTGTTGTTGAGAAACCCTTTGGTAGGGATCTAGAATCTGCAGAAGAACTCAGTACTCAGAT
TGGAGAGTTATTTGAAGAACCACAGATTTATCGTATTGATCACTATTTAGGAAAGGAACTAGTGCAAAAC
ATGTTAGTACTTCGTTTTGCAAATCGGTTCTTCTTGCCTCTGTGGAACCACAACCACATTGACAATGTGC
AGATAGTATTTAGAGAGGATTTTGGAACTGATGGTCGTGGTGGATATTTTGACCAATATGGAATTATCCG
AGATATCATTCCAAACCATCTGTTGCAGGTTCTTTGCTTGATTGCTATGGAAAAACCCGTTTCTCTCAAG
CCTGAGCACATTCGAGATGAGAAAGTGAAGGTTCTTGAATCAGTACTCCCTATTAGAGATGATGAAGTTG
TTCTTGGACAATATGAAGGCTATACAGATGACCCAACTGTACCGGACGATTCAAACACCCCGACTTTTGC
AACTACTATTCTGCGGATACACAATGAAAGATGGGAAGGTGTTCCTTTCATTGTGAAAGCAGGGAAGGCC
CTAAATTCTAGGAAGGCAGAGATTCGGGTTCAATTCAAGGATGTTCCTGGTGACATTTTCAGGAGTAAAA
AGCAAGGGAGAAACGAGTTTGTTATCCGCCTACAACCTTCAGAAGCTATTTACATGAAGCTTACGGTCAA
GCAACCTGGACTGGAAATGTCTGCAGTTCAAAGTGAACTAGACTTGTCATATGGGCAACGATATCAAGGG
ATAACCATTCCAGAGGCTTATGAGCGTCTAATTCTCGACACAATTAGAGGTGATCAACAACATTTTGTTC
GCAGAGACGAATTAAAGGCATCATGGCAAATATTCACACCACTTTTACACAAAATTGATAGAGGGGAGTT
GAAGCCGGTTCCTTACAACCCGGGAAGTAGAGGTCCTGCAGAAGCAGATGAGTTATTAGAAAAAGCTGGA
TATGTTCAAACACCCGGTTATATATGGATTCCTCCTACCTTATAGAGTGACCAAATTTCATAATAAAACA
AGGATTAGGATTATCAGGAGCTTATAAATAAGTCTTCAATAAGCTTGTGAAATTTTCGTTATAATCTCTC
TCATTTTGGGGTGTATATCAAGCATTTAAGCGCGTGTTTGACACAGTTTGTGTAATAGATTTGGCTCTGA
ATGAAAATAAACGGGAATTGTTTCTTTTTGTTTTA
FASTA definition line
>gi|603218|gb|U |MSU18238
gi number
Database identifiers
gb GenBank
emb EMBL
dbj DDBJ
sp SWISS-PROT
pdb Protein Databank
pir PIR
prf PRF
ref RefSeq
Accession number
Locus name
>

41. Entrez Genome

42. Organism Pages

43. The Map Viewer: a common platform for integrated display

44. The Map Viewer

45. Entrez PubMed

46. Online Books

47. Entrez Specialized Databases
Taxonomy
Searchable taxonomic tree having
nodes for all species with records in
an Entrez database
Online Mendelian Inheritance in Man:
A database of genetically linked
human diseases
OMIM
ProbeSet
Expression data (GEO) and microarray
datasets

48. Entrez Taxonomy

49. Entrez OMIM

50. Entrez ProbeSet

51. Trace Archive

52. Entrez Structure

53. Structure Summary
Cn3D viewer
Related Structures
Conserved Domains

54. Cn3D: Displaying Structures

55. Structural Alignment