A Field Guide to GenBank A Field Guide to GenBank and NCBI Molecular Biology and NCBI Molecular Biology

ResourcesResources

slightly modified fromslightly modified from

Peter CooperPeter Cooperftp://ftp.ncbi.nih.gov/pub/cooper/FieldGuide/ftp://ftp.ncbi.nih.gov/pub/cooper/FieldGuide/

Eric SayersEric Sayersftp://ftp.ncbi.nih.gov/pub/sayers/Field_Guide/U_Penn/ftp://ftp.ncbi.nih.gov/pub/sayers/Field_Guide/U_Penn/

• About NCBIAbout NCBI• NCBI Sequence DatabasesNCBI Sequence Databases

– Primary Database – GenBankPrimary Database – GenBank– Derivative Databases - RefSeqDerivative Databases - RefSeq

• Entrez Databases and Text Entrez Databases and Text SearchingSearching

• BLAST ServicesBLAST Services• Genomic ResourcesGenomic Resources

NCBI NCBI ResourcesResources

The National Center for The National Center for Biotechnology Biotechnology

Information (NCBI)Information (NCBI)• Created as a part of NLM in 1988Created as a part of NLM in 1988

– Establish public databasesEstablish public databases– Perform research in computational Perform research in computational

biologybiology– Develop software tools for sequence Develop software tools for sequence

analysisanalysis– Disseminate biomedical informationDisseminate biomedical information

• Tools: BLAST(1990), Entrez (1992)Tools: BLAST(1990), Entrez (1992)• GenBank (1992)GenBank (1992)• Free MEDLINE (PubMed, 1997)Free MEDLINE (PubMed, 1997)• Human genome (2001)Human genome (2001)

NCBI Home PageNCBI Home Pagehttp://www.ncbi.nlm.nih.govhttp://www.ncbi.nlm.nih.gov

To learn more, visit To learn more, visit thethe “ “Site MapSite Map” and ” and ““About NCBIAbout NCBI””web pagesweb pages

About NCBIAbout NCBI

Some NCBI Statistics….Some NCBI Statistics….Growth of GenBank

0

2000

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16000

18000

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30000

1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Ba

se P

airs

of D

NA

(m

illio

ns)

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1011121314151617181920212223

Se

qu

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ces

(mill

ion

s)

Base Pairs Sequences

Users per dayUsers per day

0

50000

100000

150000

200000

250000

1997 1998 1999 2000 2001

Christmas Day

Molecular Molecular DatabasesDatabases• Primary DatabasesPrimary Databases

– Original submissions by experimentalistsOriginal submissions by experimentalists– Database staff organize but don’t add Database staff organize but don’t add

additional informationadditional information• Example:Example: GenBankGenBank

• Derivative DatabasesDerivative Databases– Human curatedHuman curated

• compilation and correction of datacompilation and correction of data

• Example:Example: SWISS-PROT, NCBI RefSeq mRNASWISS-PROT, NCBI RefSeq mRNA

– Computationally DerivedComputationally Derived• Example:Example: UniGeneUniGene

– CombinationsCombinations• Example:Example: NCBI Genome AssemblyNCBI Genome Assembly

What is GenBank?What is GenBank? NCBI’s Primary Sequence NCBI’s Primary Sequence

DatabaseDatabase• Nucleotide only sequence database Nucleotide only sequence database • GenBank DataGenBank Data

– Direct submissions individual records (BankIt, Direct submissions individual records (BankIt, Sequin)Sequin)

– Batch submissions via email (EST, GSS, STS)Batch submissions via email (EST, GSS, STS)– ftp accounts established for sequencing centersftp accounts established for sequencing centers

• Data shared amongst three collaborating Data shared amongst three collaborating databases:databases:– GenBankGenBank– DNA Database of Japan (DDBJ). DNA Database of Japan (DDBJ). – European Molecular Biology Laboratory European Molecular Biology Laboratory

Database Database

(EMBL)(EMBL)

The International Nucleotide SequenceThe International Nucleotide SequenceDatabase CollaborationDatabase Collaboration

EBI

GenBankGenBank

DDBJDDBJ

EMBLEMBL

EMBLEMBL

Entrez

SRS

getentry

NIGNIGCIB

NCBI

NIHNIH

•Submissions•Updates •Submissions

•Updates

•Submissions•Updates

SequinBankItftp

GenBank: GenBank: NCBI’s Primary Sequence NCBI’s Primary Sequence DatabaseDatabase

• 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

Entrez Entrez NucleotideNucleotide

GenBank 71%

DDBJ 19%

EMBL 9%

RefSeq 1%

23,464,770 records

ATTGACTA

Primary vs. Derivative DatabasesPrimary vs. Derivative DatabasesACGTGC

TTGACA

CG

TG

AATTGACTA

TA

TA

GC

CG

ACGTGC

ACGTGC

AC

GT

GC

TTGACA

TTGACA

TTGACA

CG

TGA C

GTG

A

CG

TG

A

ATT

GA

CTA

ATTGACTA ATTGACTA

ATTGACTA

TATAGCCG

TATAGCCG

TATA

GC

CG

TATAGCCG

GenBank

TATAGCCG TATAGCCGTATAGCCGTATAGCCG

ATGA

CATT

GAGA

ATTATT

CC GAGA

ATTC

CGAGA

ATTATT

CC GAGA

ATTC

C

SequencingCenters

GAGA

ATTC

C GAGA

ATTC

C

UniGene

RefSeq

GenomeAssembly

Labs

Curators

Algorithms

TATAGCCGAGCTCCGATACCGATGACAA

Traditional GenBank Traditional GenBank DivisionsDivisions

BCT Bacterial and Archeal INV InvertebrateMAM Mammalian (ex. ROD and PRI)PHG PhagePLN Plant and FungalPRI PrimateROD RodentSYN Synthetic (cloning vectors)VRL ViralVRT Other Vertebrate

•Direct Submissions (Sequin and BankIt)•Accurate•Well characterized

A Traditional GenBank A Traditional GenBank RecordRecordLocus Field Molecule Type

GenBank Division

Modification DateDefinition Line

Accession NumberVersion

Taxonomy

GI (GenInfo)Keywords

A Traditional GenBank A Traditional GenBank RecordRecord

Bulk Sequence Bulk Sequence Divisions of GenBankDivisions of GenBank

EST Expressed Sequence Tag STS Sequence Tagged SiteGSS Genome Survey SequenceHTG High Throughput GenomicHTC High Throughput cDNA

•Batch Submissions (email and ftp)•Inaccurate•Poorly Characterized

Organization of GenBankOrganization of GenBank

EST 67%

GSS 19%

Traditional 8%PAT 4%

23,087,196 records

STS, HTG, HTC 2%

11 Traditional Divisions

5 Bulk Divisions

1 Patent Division

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

What is UniGene?What is UniGene?

Organisms RepresentedOrganisms Representedin UniGenein UniGene

Genome Genome Sequencing Sequencing

Draft Sequence (HTG division)

shredding

Whole BAC insert (or genome)

cloning isolating

assembly

sequencing

GSS divisionor trace archive

Working Draft SequenceWorking Draft Sequence

gaps

phase 1

phase 2

phase 3 ROD

Acc = AC109609.1

Acc =AC109609.6

Acc = AC109609.10

HTG

HTG

HTG Division: HTG Division: HHigh igh TThroughput hroughput GGenomeenome

HTG Division: HTG Division: HHigh igh TThroughput hroughput GGenomeenome

NCBI’s Third Party Annotation NCBI’s Third Party Annotation (TPA) Database (TPA) Database

• NCBI now accepts the submission of NCBI now accepts the submission of new annotations of new annotations of existingexisting GenBank GenBank sequences;sequences;

• Facilitates the annotation of Facilitates the annotation of genomes by experts;genomes by experts;

NEW

A Sample TPA record A Sample TPA record

RefSeq: RefSeq: NCBI’s Derivative Sequence NCBI’s Derivative Sequence

DatabaseDatabase• Curated transcripts and proteinsCurated transcripts and proteins

– reviewedreviewed– human, mouse, rat, fruit fly, zebrafish, arabidopsishuman, mouse, rat, fruit fly, zebrafish, arabidopsis

• Human model transcripts and Human model transcripts and proteinsproteins

• Assembled Genomic Regions Assembled Genomic Regions (contigs)(contigs)– draft human genomedraft human genome– mouse genomemouse genome

• Chromosome recordsChromosome records– MicrobialMicrobial– viralviral– organelleorganelle

The RefSeq Accession The RefSeq Accession NumbersNumbersmRNAs and Proteins

NM_123456 Curated mRNANP_123456 Curated ProteinNR_123456 Curated non-coding RNAXM_123456 Predicted Transcript (human, mouse)XP_123456 Predicted Protein (human, mouse)XR_123456 Predicted non-coding RNAGene RecordsNG_ 123456 Reference Genomic Sequence (human)AssembliesNT_ 123456 Contig (Mouse and Human)NW_123456 Supercontig (Mouse)NC_ 123456 Chromosome (Microbial,Viral,Arabidopsis )NR_ 123456 Interim Identifier for Microbial

Chromosomes

humanmouseratfruit flyzebrafishArabidopsis

Curated RefSeq Records: Curated RefSeq Records: NM_, NM_, NP_NP_

Entrez:Entrez:Linking and NeighboringLinking and Neighboring

The Entrez DatabasesThe Entrez Databases

The The (ever)(ever) Expanding Entrez Expanding Entrez SystemSystem

Nucleotide

Protein

Structure

PubMed

PopSet

Genome

OMIM

Taxonomy

Books

ProbeSet

3D Domains

UniSTS

SNP

CDD

Entrez

UniGeneJournals

PubMedCentral

glucose 6 phosphate dehydrogenase

Entrez NucleotidesEntrez Nucleotides

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

glucose 6 phosphate dehydrogenase

Entrez Nucleotides: Limits Entrez Nucleotides: Limits AccessionAll FieldsAuthor NameEC/RN NumberFeature keyFilterGene NameIssueJournal NameKeywordModification DateOrganismPage NumberPrimary AccessionPropertiesProtein NamePublication DateSeqID StringSequence LengthSubstance NameText WordTitle WordUidVolume

Entrez Nucleotides: Entrez Nucleotides: Preview/IndexPreview/Index

Adding Terms: Adding Terms: Preview/IndexPreview/Index

AccessionAll FieldsAuthor NameEC/RN NumberFeature keyFilterGene NameIssueJournal NameKeywordModification DateOrganismPage NumberPrimary AccessionPropertiesProtein NamePublication DateSeqID StringSequence Length. . .

Plant G6PD Plant G6PD mRNAsmRNAs

Display: Display: Formats, Links, and NeighborsFormats, Links, and Neighbors

SummaryBriefASN.1FASTAXMLGenBankGI listLinkOutNucleotide NeighborsGenome LinksProbeSet LinksOMIM LinksPopSet LinksProtein LinksPubMed LinksSNP LinksStructure LinksTaxonomy LinksUniSTS Links

>gi|603218|gb|U18238.1|MSU18238 Medicago sativa glucose-6-phosphate dehydCCACCAGATATAATTAAGTAGATCAGAGTAGAAGAAGATGGGAACAAATGAATGGCATGTAGAAAGAAGAGATAGCATAGGTACTGAATCTCCTGTAGCAAGAGAGGTACTTGAAACTGGCACACTCTCTATTGTTGTGCTTGGTGCTTCTGGTGATCTTGCCAAGAAGAAGACTTTTCCTGCACTTTTTCACTTATATAAACAGGAATTGTTGCCACCTGATGAAGTTCACATTTTTGGCTATGCAAGGTCAAAGATCTCCGATGATGAATTGAGAAACAAATTGCGTAGCTATCTTGTTCCAGAGAAAGGTGCTTCTCCTAAACAGTTAGATGATGTATCAAAGTTTTTACAATTGGTTAAATATGTAAGTGGCCCTTATGATTCTGAAGATGGATTTCGCTTGTTGGATAAAGAGATTTCAGAGCATGAATATTTGAAAAATAGTAAAGAGGGTTCATCTCGGAGGCTTTTCTATCTTGCACTTCCTCCTTCAGTGTATCCATCCGTTTGCAAGATGATCAAAACTTGTTGCATGAATAAATCTGATCTTGGTGGATGGACACGCGTTGTTGTTGAGAAACCCTTTGGTAGGGATCTAGAATCTGCAGAAGAACTCAGTACTCAGATTGGAGAGTTATTTGAAGAACCACAGATTTATCGTATTGATCACTATTTAGGAAAGGAACTAGTGCAAAACATGTTAGTACTTCGTTTTGCAAATCGGTTCTTCTTGCCTCTGTGGAACCACAACCACATTGACAATGTGCAGATAGTATTTAGAGAGGATTTTGGAACTGATGGTCGTGGTGGATATTTTGACCAATATGGAATTATCCGAGATATCATTCCAAACCATCTGTTGCAGGTTCTTTGCTTGATTGCTATGGAAAAACCCGTTTCTCTCAAGCCTGAGCACATTCGAGATGAGAAAGTGAAGGTTCTTGAATCAGTACTCCCTATTAGAGATGATGAAGTTGTTCTTGGACAATATGAAGGCTATACAGATGACCCAACTGTACCGGACGATTCAAACACCCCGACTTTTGCAACTACTATTCTGCGGATACACAATGAAAGATGGGAAGGTGTTCCTTTCATTGTGAAAGCAGGGAAGGCCCTAAATTCTAGGAAGGCAGAGATTCGGGTTCAATTCAAGGATGTTCCTGGTGACATTTTCAGGAGTAAAAAGCAAGGGAGAAACGAGTTTGTTATCCGCCTACAACCTTCAGAAGCTATTTACATGAAGCTTACGGTCAAGCAACCTGGACTGGAAATGTCTGCAGTTCAAAGTGAACTAGACTTGTCATATGGGCAACGATATCAAGGGATAACCATTCCAGAGGCTTATGAGCGTCTAATTCTCGACACAATTAGAGGTGATCAACAACATTTTGTTCGCAGAGACGAATTAAAGGCATCATGGCAAATATTCACACCACTTTTACACAAAATTGATAGAGGGGAGTTGAAGCCGGTTCCTTACAACCCGGGAAGTAGAGGTCCTGCAGAAGCAGATGAGTTATTAGAAAAAGCTGGATATGTTCAAACACCCGGTTATATATGGATTCCTCCTACCTTATAGAGTGACCAAATTTCATAATAAAACAAGGATTAGGATTATCAGGAGCTTATAAATAAGTCTTCAATAAGCTTGTGAAATTTTCGTTATAATCTCTCTCATTTTGGGGTGTATATCAAGCATTTAAGCGCGTGTTTGACACAGTTTGTGTAATAGATTTGGCTCTGAATGAAAATAAACGGGAATTGTTTCTTTTTGTTTTA

>

FASTA definition line>gi|603218|gb|U18238.1|MSU18238

gi number

Database identifiersgb GenBankemb EMBLdbj DDBJsp SWISS-PROTpdb Protein Databankpir PIRprf PRFref RefSeq

Accession number

Locus name

Entrez GenomeEntrez Genome

Organism Organism PagesPages

The Map Viewer: The Map Viewer: a common platform for integrated displaya common platform for integrated display

The Map Viewer The Map Viewer

Entrez PubMedEntrez PubMed

Online BooksOnline Books

Entrez Specialized Entrez Specialized DatabasesDatabases

Taxonomy

OMIM

ProbeSet

Searchable taxonomic tree havingnodes for all species with records inan Entrez database

Online Mendelian Inheritance in Man:A database of genetically linkedhuman diseases

Expression data (GEO) and microarraydatasets

Entrez Taxonomy Entrez Taxonomy

Entrez OMIMEntrez OMIM

Entrez Entrez ProbeSetProbeSet

Trace ArchiveTrace Archive

Entrez StructureEntrez Structure

Structure Structure SummarySummary

Cn3D viewer

Related Structures

Conserved Domains

Cn3D: Displaying StructuresCn3D: Displaying Structures

Structural Structural AlignmentAlignment