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/
NCBI Resources
• About NCBI
• NCBI Sequence Databases
– Primary Database – GenBank
– Derivative Databases - RefSeq
• Entrez Databases and Text Searching
• BLAST Services
• Genomic Resources
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)
NCBI Home Page
http://www.ncbi.nlm.nih.gov
To learn more, visit the
“Site Map” and
“About NCBI”
web pages
About NCBI
Some NCBI Statistics….
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
0
1982
30000
28000
26000
24000
22000
20000
18000
16000
14000
12000
10000
Base Pairs
Sequences
8000
6000
4000
2000
0
1984
1986
1988
1990
1992
1994
1996
1998
2000
2002
Base Pairs of DNA (millions)
Sequences (millions)
Growth of GenBank
Users per day
250000
1997
1998
1999
2000
200000
150000
100000
50000
Christmas Day
0
2001
Molecular Databases
• Primary 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
What is GenBank?
NCBI’s Primary Sequence Database
• Nucleotide only sequence database
• GenBank Data
– Direct submissions individual records (BankIt,
Sequin)
– Batch submissions via email (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)
The International Nucleotide Sequence
Database Collaboration
NIH
Sequin
BankIt
ftp
Entrez
NCBI
GenBank
•Submissions
•Updates
•Submissions
•Updates
EMBL
CIB
NIG
DDBJ
•Submissions
•Updates
getentry
EBI
SRS
EMBL
GenBank: NCBI’s Primary Sequence Database
Release 133
22,318,883
28,507,990,166
110,000 +
December 2002
Records
Nucleotides
Species
• full release every two months
• incremental and cumulative updates daily
• available only through internet
ftp://ftp.ncbi.nih.gov/genbank/
>90 Gigabytes of data
Entrez
Nucleotide
RefSeq 1%
EMBL 9%
DDBJ 19%
GenBank 71%
23,464,770 records
Primary vs. Derivative Databases
Curators
RefSeq
Sequencing
Centers
TATAGCCG
AGCTCCGATA
CCGATGACAA
Labs
Genome
Assembly
TATAGCCG
TATAGCCG
TATAGCCG
TATAGCCG
GenBank
UniGene
Algorithms
Traditional GenBank Divisions
•Direct Submissions (Sequin and BankIt)
•Accurate
•Well characterized
BCT
INV
MAM
PHG
PLN
PRI
ROD
SYN
VRL
VRT
Bacterial and Archeal
Invertebrate
Mammalian (ex. ROD and PRI)
Phage
Plant and Fungal
Primate
Rodent
Synthetic (cloning vectors)
Viral
Other Vertebrate
A Traditional GenBank Record
Locus Field
Molecule Type
Definition Line
Accession Number
Version GI (GenInfo)
Keywords
Taxonomy
Modification Date
GenBank Division
A Traditional GenBank Record
Bulk Sequence Divisions
of GenBank
•Batch Submissions (email and ftp)
•Inaccurate
•Poorly Characterized
EST
STS
GSS
HTG
HTC
Expressed Sequence Tag
Sequence Tagged Site
Genome Survey Sequence
High Throughput Genomic
High Throughput cDNA
Organization of GenBank
11 Traditional Divisions
Traditional 8%
PAT 4%
1 Patent Division
STS, HTG, HTC 2%
GSS 19%
EST 67%
5 Bulk Divisions
23,087,196 records
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
Organisms Represented
in UniGene
Genome Sequencing
Whole BAC insert (or genome)
shredding
sequencing
GSS division
or trace archive
cloning isolating
assembly
Draft Sequence (HTG
division)
Working Draft Sequence
gaps
HTG Division:
High Throughput Genome
phase 1
HTG
phase 2
HTG
phase 3
ROD
Acc = AC109609.1
Acc =AC109609.6
Acc = AC109609.10
HTG Division:
High Throughput Genome
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;
A Sample TPA record
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
The RefSeq Accession Numbers
mRNAs and Proteins
NM_123456
NP_123456
NR_123456
XM_123456
XP_123456
XR_123456
Gene Records
NG_ 123456
Assemblies
NT_ 123456
NW_123456
NC_ 123456
NR_ 123456
human
Curated mRNA
mouse
rat
Curated Protein
fruit fly
Curated non-coding RNA
zebrafish
Predicted Transcript (human, mouse)
Arabidopsis
Predicted Protein (human, mouse)
Predicted non-coding RNA
Reference Genomic Sequence (human)
Contig (Mouse and Human)
Supercontig (Mouse)
Chromosome (Microbial,Viral,Arabidopsis )
Interim Identifier for Microbial
Chromosomes
Curated RefSeq Records: NM_, NP_
Entrez:
Linking and Neighboring
The Entrez Databases
The
(ever)
Journals
Expanding Entrez
System
UniGene
Books
PubMed
Central
SNP
PubMed
UniSTS
Nucleotide
Protein
PopSet
ProbeSet
Entrez
Genome
Structure
Taxonomy
CDD
3D Domains
OMIM
Entrez Nucleotides
glucose 6 phosphate dehydrogenase
Document Summaries:
glucose 6 phosphate dehydrogenase[All Fields] = 748 hits
Entrez Nucleotides: Limits
Accession
All Fields
Author Name
EC/RN Number
glucose 6 phosphate dehydrogenase
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
Entrez Nucleotides:
Preview/Index
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
. . .
Plant G6PD mRNAs
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
>gi|603218|gb|U18238.1|MSU18238 Medicago sativa glucose-6-phosphate dehyd
CCACCAGATATAATTAAGTAGATCAGAGTAGAAGAAGATGGGAACAAATGAATGGCATGTAGAAAGAAGA
GATAGCATAGGTACTGAATCTCCTGTAGCAAGAGAGGTACTTGAAACTGGCACACTCTCTATTGTTGTGC
TTGGTGCTTCTGGTGATCTTGCCAAGAAGAAGACTTTTCCTGCACTTTTTCACTTATATAAACAGGAATT
GTTGCCACCTGATGAAGTTCACATTTTTGGCTATGCAAGGTCAAAGATCTCCGATGATGAATTGAGAAAC
AAATTGCGTAGCTATCTTGTTCCAGAGAAAGGTGCTTCTCCTAAACAGTTAGATGATGTATCAAAGTTTT
TACAATTGGTTAAATATGTAAGTGGCCCTTATGATTCTGAAGATGGATTTCGCTTGTTGGATAAAGAGAT
TTCAGAGCATGAATATTTGAAAAATAGTAAAGAGGGTTCATCTCGGAGGCTTTTCTATCTTGCACTTCCT
>
CCTTCAGTGTATCCATCCGTTTGCAAGATGATCAAAACTTGTTGCATGAATAAATCTGATCTTGGTGGAT
GGACACGCGTTGTTGTTGAGAAACCCTTTGGTAGGGATCTAGAATCTGCAGAAGAACTCAGTACTCAGAT
gi number
TGGAGAGTTATTTGAAGAACCACAGATTTATCGTATTGATCACTATTTAGGAAAGGAACTAGTGCAAAAC
Locus name
ATGTTAGTACTTCGTTTTGCAAATCGGTTCTTCTTGCCTCTGTGGAACCACAACCACATTGACAATGTGC
AGATAGTATTTAGAGAGGATTTTGGAACTGATGGTCGTGGTGGATATTTTGACCAATATGGAATTATCCG
Database identifiers
AGATATCATTCCAAACCATCTGTTGCAGGTTCTTTGCTTGATTGCTATGGAAAAACCCGTTTCTCTCAAG
Accession number
gb
GenBank
CCTGAGCACATTCGAGATGAGAAAGTGAAGGTTCTTGAATCAGTACTCCCTATTAGAGATGATGAAGTTG
TTCTTGGACAATATGAAGGCTATACAGATGACCCAACTGTACCGGACGATTCAAACACCCCGACTTTTGC
emb
EMBL
AACTACTATTCTGCGGATACACAATGAAAGATGGGAAGGTGTTCCTTTCATTGTGAAAGCAGGGAAGGCC
dbj
DDBJ
CTAAATTCTAGGAAGGCAGAGATTCGGGTTCAATTCAAGGATGTTCCTGGTGACATTTTCAGGAGTAAAA
AGCAAGGGAGAAACGAGTTTGTTATCCGCCTACAACCTTCAGAAGCTATTTACATGAAGCTTACGGTCAA
sp
SWISS-PROT
GCAACCTGGACTGGAAATGTCTGCAGTTCAAAGTGAACTAGACTTGTCATATGGGCAACGATATCAAGGG
pdb
Protein Databank
ATAACCATTCCAGAGGCTTATGAGCGTCTAATTCTCGACACAATTAGAGGTGATCAACAACATTTTGTTC
GCAGAGACGAATTAAAGGCATCATGGCAAATATTCACACCACTTTTACACAAAATTGATAGAGGGGAGTT
pir
PIR
GAAGCCGGTTCCTTACAACCCGGGAAGTAGAGGTCCTGCAGAAGCAGATGAGTTATTAGAAAAAGCTGGA
prf
PRF
TATGTTCAAACACCCGGTTATATATGGATTCCTCCTACCTTATAGAGTGACCAAATTTCATAATAAAACA
ref
RefSeq
AGGATTAGGATTATCAGGAGCTTATAAATAAGTCTTCAATAAGCTTGTGAAATTTTCGTTATAATCTCTC
TCATTTTGGGGTGTATATCAAGCATTTAAGCGCGTGTTTGACACAGTTTGTGTAATAGATTTGGCTCTGA
ATGAAAATAAACGGGAATTGTTTCTTTTTGTTTTA
FASTA definition line
>gi|603218|gb|U18238.1|MSU18238
Entrez Genome
Organism
Pages
The Map Viewer:
a common platform for integrated display
The Map Viewer
Entrez PubMed
Online Books
Entrez Specialized Databases
Taxonomy
Searchable taxonomic tree having
nodes for all species with records in
an Entrez database
OMIM
Online Mendelian Inheritance in Man:
A database of genetically linked
human diseases
ProbeSet
Expression data (GEO) and microarray
datasets
Entrez Taxonomy
Entrez OMIM
Entrez
ProbeSet
Trace Archive
Entrez Structure
Structure Summary
Cn3D viewer
Related Structures
Conserved Domains
Cn3D: Displaying Structures
Structural Alignment