NCBI FieldGuide NCBI Molecular Biology Resources A Field Guide University of MassachusettsAugust 2-3, 2005.

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NCBI Molecular Biology Resources

A Field Guide

University of MassachusettsAugust 2-3, 2005

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e• The NCBI Entrez System

• NCBI Sequence Databases– Primary data: GenBank– Derivative data: RefSeq, Gene, Genome – Beyond Refseq: UniGene, Trace Archive

• NCBI Genomic Resources** Intermission **

• BLAST

• Protein Structure and Function

• Sequence polymorphisms and phenotypes

NCBI Resources

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eThe National Institutes of Health

Bethesda, MD

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eThe National Center for

Biotechnology Information

• 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

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eWeb

Access

BLAST

VAST

Entrez

Text

Sequence

Structure

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NCBI Web Traffic

Christmas and New Year’s Day

User’s per day

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The NCBI ftp site

30,000 files per day620 Gigabytes per day

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What does NCBI do?

• NCBI accepts submissions of primary data

• NCBI develops tools to analyze these data

• NCBI uses these tools to create derivative databases based on the primary data

• NCBI provides free search, link, and retreival of these data, primarily through the Entrez system

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Types of Databases

• Primary Databases– Original submissions by experimentalists– Content controlled by the submitter

• Examples: GenBank, SNP, GEO, PubChem Substance

• Derivative Databases– Built from primary data– Content controlled by third party (NCBI)

• Examples: Refseq, TPA, RefSNP, UniGene, Protein, Structure, Conserved Domain, PubChem Compound

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Primary vs. Derivative Databases

ACGTGC

CG

TG

AATTGACTAACGTGCA

CG

TG

C

TTGACA

TATAGCCG

GenBank

SequencingCenters

GAGA

ATTC

C GAGA

ATTC

C UniGene

RefSeq:LocusLink andGenomes Pipelines

RefSeq:Annotation Pipeline

Labs

Curators

Algorithms

TATAGCCGAGCTCCGATACCGATGACAA

Updated ONLY by submitters

EST UniSTS

STS

GSS

HTG

Updated continuall

y by NCBI

PRI ROD PLN MAM BCT

INV VRT PHG VRL

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What is Entrez?

• A system of 29 linked databases

• A text search engine

• A tool for finding biologically linked data

• A retrieval engine

• A virtual workspace for manipulating large datasets

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The Entrez System: Text Searches

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Entrez Databases

• Each record is assigned a UID– unique integer identifier for internal tracking– GI number for Nucleotide

• Each record is given a Document Summary– a summary of the record’s content (DocSum)

• Each record is assigned links to biologically related UIDs

• Each record is indexed by data fields– [author], [title], [organism], and many others

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Entrez Taxonomy

The backbone of NCBI

[organism]

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An Entrez Database - Nucleotide

• GenBank: Primary Data (97.9%)– original submissions by experimentalists– submitters retain editorial control of records– archival in nature

• RefSeq: Derivative Data (2.1%)– curated by NCBI staff– NCBI retains editorial control of records– record content is updated continually

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Entrez Nucleotide

Primary Data • DDBJ / EMBL / GenBank 56,865,268

Derivative Data• RefSeq 1,226,084

• PDB 5,973• Third Party Annotation 4,650

Total 58,101,975

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eWhat is GenBank? NCBI’s Primary Sequence

Database• Nucleotide only sequence database • Archival in nature• Each record is assigned a stable accession number• GenBank Data

– Direct submissions (traditional records )– Batch submissions (EST, GSS, STS)– ftp accounts (genome data)

• Three collaborating databases– GenBank– DNA Database of Japan (DDBJ) – European Molecular Biology Laboratory (EMBL)

Database

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EBI

GenBankGenBank

DDBJDDBJ

EMBLEMBL

EMBLEMBL

Entrez

SRS

getentry

NIGNIGCIB

NCBI

NIHNIH

•Submissions•Updates •Submissions

•Updates

•Submissions•Updates

The International Sequence Database Collaboration

SequinBankItftp

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• full release every two months• incremental and cumulative updates daily• available only through internet

ftp://ftp.ncbi.nih.gov/genbank/

Release 148 June 2005 45,236,251 Records 49,398,852,122 Nucleotides >140,000 Species 172 Gigabytes 785 files

GenBank Releases

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BasepairsRecords

The Growth of GenBank

Release 148: 45.2 million records 49.4 billion nucleotides

Average doubling time ≈ 14 months*

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GenBank Divisions

PRI (28) Primate ROD (14) Rodent PLN (13) Plant and FungalBCT (10) Bacterial/ArchealINV (7) InvertebrateVRT (7) Other Vertebrate VRL (4) ViralMAM (2) MammalianPHG (1) PhageSYN (1) SyntheticUNA (1) Unannotated

•Direct Submissions (Sequin/Bankit)•Accurate (~1 error per 10,000 bp)•Well characterized•Organized by taxonomy

EST (349) Expressed Sequence Tag GSS (120) Genome Survey SequenceHTG (62) High Throughput GenomicHTC (6) High Throughput cDNA STS (5) Sequence Tagged Site

•From sequencing projects•Batch submissions (ftp/email) •Inaccurate•Poorly Characterized•Organized by sequence type

Traditional

Bulk

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A Traditional GenBank RecordLOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.ACCESSION AY182241VERSION AY182241.2 GI:32265057KEYWORDS .SOURCE Malus x domestica (cultivated apple) ORGANISM Malus x domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.REFERENCE 1 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Cloning and functional expression of an (E,E)-alpha-farnesene synthase cDNA from peel tissue of apple fruit JOURNAL Planta 219, 84-94 (2004)REFERENCE 2 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Direct Submission JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab, USDA-ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD 20705, USAREFERENCE 3 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Direct Submission JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab, USDA-ARS, 10300 Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD 20705, USA REMARK Sequence update by submitterCOMMENT On Jun 26, 2003 this sequence version replaced gi:27804758.FEATURES Location/Qualifiers source 1..1931 /organism="Malus x domestica" /mol_type="mRNA" /cultivar="'Law Rome'" /db_xref="taxon:3750" /tissue_type="peel" gene 1..1931 /gene="AFS1" CDS 54..1784 /gene="AFS1" /note="terpene synthase" /codon_start=1 /product="(E,E)-alpha-farnesene synthase" /protein_id="AAO22848.2" /db_xref="GI:32265058" /translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI LSLLFQPLVN"ORIGIN 1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat 61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg 121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt 181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga 241 agctgtctga gaagttaata gaagaagtta agatttatat atctgctgaa acaatggatt

1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt 1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa 1921 aaaaaaaaaa a//

Header

Feature Table

Sequence

The Flatfile Format

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An Example Record – M17755

Field Indexed Terms

[primary accession] M17755[title] Homo sapiens thyroid peroxidase (TPO) mRNA…[organism] Homo sapiens[sequence length] 3060[modification date] 1999/04/26[properties] biomol mrna

gbdiv prisrcdb genbank

Indexing for Nucleotide UID 4680720

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M17755: Feature Table

CDS position in bp

TPO [gene name]

thyroiditis[text word]

thyroid peroxidase[protein name]

protein accession

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Sequence: 99.99% Accurate

The sequence itselfis not indexed…

Use BLAST for that!

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Entrez Protein

• GenPept (DDBJ, EMBL, GenBank) 4,444,405• RefSeq 1,753,167• PIR 222,395• Swiss Prot 189,005• PDB 68,621• PRF 12,079• Third Party Annotation 4,219 Total 6,693,891

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Protein Sources and Links

PIR

RefSeq

SWISS-PROT

GenPept

NM_000537

M17755

no mRNA!

no mRNA!

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Sequence Revisions

Version and GI change only if the sequence changes

The accession number always retrieves the most recent version

First seen at NCBI, not first seen at GenBank!

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eUpdate without a Sequence

Change

June 15, 1989!

GenBank cameto NCBI in 1992!

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Update with a Sequence Change

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GenBank File Formats

ASN.1 – The Raw Data

XML (4 flavors)

FASTA

flat file

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/************************************************************************** asn2ff.c* convert an ASN.1 entry to flat file format, using the FFPrintArray. ***************************************************************************/#include <accentr.h>#include "asn2ff.h"#include "asn2ffp.h"#include "ffprint.h"#include <subutil.h>#include <objall.h>#include <objcode.h>#include <lsqfetch.h>#include <explore.h>

#ifdef ENABLE_ID1#include <accid1.h>#endif

FILE *fpl;

Args myargs[] = {{"Filename for asn.1 input","stdin",NULL,NULL,TRUE,'a',ARG_FILE_IN,0.0,0,NULL},{"Input is a Seq-entry","F", NULL ,NULL ,TRUE,'e',ARG_BOOLEAN,0.0,0,NULL},{"Input asnfile in binary mode","F",NULL,NULL,TRUE,'b',ARG_BOOLEAN,0.0,0,NULL},{"Output Filename","stdout", NULL,NULL,TRUE,'o',ARG_FILE_OUT,0.0,0,NULL},{"Show Sequence?","T", NULL ,NULL ,TRUE,'h',ARG_BOOLEAN,0.0,0,NULL},

Toolbox Sources

ftp> open ftp.ncbi.nih.gov..ftp> cd toolboxftp> cd ncbi_tools

ftp://ftp.ncbi.nlm.gov/toolbox/ncbi_tools

NCBI Toolbox

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Text Searches in Entrez

term1[limit] OP term2[limit] OP …

limit = Entrez indexing field (organism, author, …)

op = AND, OR, NOT

where

Organism? [ organism ]Journal? [ journal ]User compounds? search as phraseAuthor? [author]else [All Fields]

term1 term2

If no [limit] is specified…

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Entrez Tabs

Limits Provides a simple form for applying commonly used Entrez limits

Preview/Index Allows access to the full indexing of each Entrez database and aids in constructing complex queries

History Provides access to previous searches in the current Entrez database

Clipboard A temporary storage area for selected records

Details Displays the detailed parsing of the current Entrez query, and lists errors and terms without matches

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Programming Entrez: E-Utilities

ESearch

EPost

ESummary

Entrez query UID list or History

Document summaries

http://www.ncbi.nih.gov/entrez/query/static/eutils_help.html

History

UID list or History

UID list

EFetch Formatted dataUID list or History

ELinkUID list or History UID list or History

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Finding Primary Sequences

• Search Entrez Nucleotide– 97.9% GenBank (primary data)– 2.1% RefSeq (curated data)

M17755 [primary accession] TPO [gene name]thyroid peroxidase [title] thyroiditis [text word]Homo sapiens [organism] thyroid peroxidase [protein name]3060 [sequence length] 1999/04/26 [modification date]biomol mrna [properties] gbdiv pri [properties]srcdb genbank [properties]

Possible queries we’ve seen so far…

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A Starting Query

Find nucleotide records for human thyroid peroxidase

(("Homo sapiens“[Organism] OR human[All Fields]) AND thyroid peroxidase[All Fields])

human thyroid peroxidase

human[organism] AND thyroid peroxidase

("Homo sapiens“[Organism] AND thyroid peroxidase[All Fields])

309 records

298 records

Field Limit!

11 records aren’t human sequences!!

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Limit by Title and Database

#1: thyroid peroxidase AND human[orgn] 298#2: thyroid peroxidase[title] AND human[orgn] 169

#3: #2 AND srcdb refseq[properties] 5#4: #2 AND srcdb ddbj/embl/genbank[properties] 164

Entrez Nucleotide

GenBank srcdb ddbj/embl/genbank[properties]

RefSeq srcdb refseq[properties]

primary data

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Limit by Genbank Division

EST Division gbdiv est[prop]

Primate Division gbdiv pri[prop]

#1: thyroid peroxidase AND human[orgn] 298

#2: thyroid peroxidase[title] AND human[orgn] 169

#3: #2 AND srcdb refseq[properties] 5#4: #2 AND srcdb ddbj/embl/genbank[properties] 164

#5: #4 AND gbdiv est[prop] 20#6: #4 AND gbdiv pri[prop] 144

traditional GenBank records

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Limit by Biomolecule Type

Genomic DNA biomol genomic[prop]

cDNA biomol mrna[prop]

#1: thyroid peroxidase AND human[orgn] 298#2: thyroid peroxidase[title] AND human[orgn] 169#3: #2 AND srcdb refseq[properties] 5#4: #2 AND srcdb ddbj/embl/genbank[properties] 164#5: #2 AND gbdiv est[prop] 20#6: #2 AND gbdiv pri[prop] 144

#7: #6 AND biomol genomic[prop] 26#8: #6 AND biomol mrna[prop] 118

mRNA / cDNA

genomic DNA

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Limit by Protein Namethyroid peroxidase[protein name] AND human[orgn] AND gbdiv pri[prop] AND biomol mrna[prop]

118 records [title] 4 records [protein name]

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Entrez Document Summaries

Click the accession to view the record

Links menu

Links to other Entrez databasescomputed for M17755

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Entrez Links for GI 4680720

Microarray datasets for M17755

Gene annotation based on M17755

DNA/RNA sequences similar to M17755

Human phenotypes involving TPO

Protein translation of M17755

Literature abstracts about M17755

Sequence polymorphisms in M17755

Source organism of M17755

STS markers in the TPO gene

TPO links beyond NCBI

Full text online articles about M17755

All polymorphisms in the TPO gene

Graphical view of TPO gene annotation

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Viewing M17755

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eGenBank Sequences for Human

TPO

Which one is the best sequence???

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• Non-redundant  • Explicitly linked nucleotide and protein sequences• Updated to reflect current sequence data and biology• Validated by hand • Format consistency• Distinct accession series • Stewardship by NCBI staff and collaborators

ftp://ftp.ncbi.nih.gov/refseq/release

RefSeq: NCBI’s Derivative Sequence Database

RefSeq Benefits

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RefSeq: NCBI’s Derivative Sequence Database

• Curated transcripts and proteins– NM_123456 NP_123456– NR_123456 (non-coding RNA)

• Model transcripts and proteins– XM_123456 XP_123456

– XR_123456 (non-coding RNA)

• Assembled Genomic Regions (contigs)– NT_123456 (BAC clones)– NW_123456 (WGS)

• Other Genomic Sequence– NG_123456 (complex regions, pseudogenes)

– NZ_ABCD12345678 (WGS) ZP_123456

• Chromosome records in Entrez Genome– NC_123456 (chromosome; microbial or organelle genome)

Nucleotide

Protein

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Creating NM Records

Longest mRNA

NMs must have cDNA support

Genome annotation

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NM/NP Records in Entrez

COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from M17755.2 and AW874082.1. On Feb 25, 2003 this sequence version replaced gi:21361188.

NM_000547: variant 1

COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from J02970.1, AW874082.1 and M17755.2.

NM_175719: variant 2 EST that completes 3’ end

Nucleotide

Protein

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Genomic DNAGenomic DNA((NCNC, , NT, NWNT, NW))

Model mRNAModel mRNA (XM)(XM)(XR)(XR)

Curated mRNACurated mRNA (NM)(NM)(NR)(NR)

Model protein Model protein (XP)(XP)

Annotating the Gene

Curated ProteinCurated Protein (NP)(NP)

Scanning....

= ?= !

GenbankSequences

RefSeq

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Entrez Gene and RefSeq

• Entrez Gene is the central depository for information about a gene available at NCBI, and often provides links to sites beyond NCBI

• Entrez Gene includes records for organisms that have NCBI Reference Sequences (RefSeqs)

• Entrez Gene records contain RefSeq mRNAs, proteins, and genomic DNA (if known) for a gene locus, plus links to other Entrez databases • NCBI RefSeqs are based on primary sequence data in GenBank

GenBank RefSeq Gene

Nucleotide

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Entrez Gene: RefSeq Annotations

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NM/NP Records in Entrez Gene

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Entrez Gene RefSeq Graphics

NM NP

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What about LOC440844?

Entrez Gene

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BLAST Results for XM_496543Is there any GenBank support for this mRNA?

no full-length hit

srcdb ddbj/embl/genbank[prop] AND biomol mrna[prop]

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The Perils of the XM

XM records are models based only on genomic sequence, and are subjectto revision or removal with each new build of that genome.

Query= gi|20850420|ref|XM_124429.1| Mus musculus expressed sequence AA553001 (AA553001), mRNA

gi|19527087|ref|NM_133873.1|      Mus musculus DNA segment, Chr 4, Wayne State University 114, expressed (D4Wsu114e), mRNA Length=1898 Score = 3701.55 bits (1867), Expect = 0 Identities = 1870/1871 (99%), Gaps = 0/1871 (0%) Strand=Plus/Plus

BLAST the XM against the RefSeq database to look for a replacement:

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Eukaryotic NM/XM RecordsBos taurus: 37541Oryza sativa (japonica cultivar-group): 36836Danio rerio: 30577Homo sapiens: 29261Arabidopsis thaliana: 28953Mus musculus: 27033Rattus norvegicus: 23975Pan troglodytes: 21810Caenorhabditis elegans: 21124Drosophila melanogaster: 19412Aspergillus nidulans FGSC A4: 18951Gallus gallus: 18120Canis familiaris: 16891Anopheles gambiae str. PEST: 15328Plasmodium chabaudi: 14747Candida albicans SC5314: 13672Dictyostelium discoideum: 13570Ustilago maydis 521: 13044Plasmodium berghei: 11778Gibberella zeae PH-1: 11640Magnaporthe grisea 70-15: 11109Neurospora crassa: 10079Aspergillus fumigatus Af293: 9923Entamoeba histolytica HM-1:IMSS: 9772Cryptococcus neoformans var. neoformans JEC21: 6594

Giardia lamblia ATCC 50803: 6569Yarrowia lipolytica CLIB99: 6521Debaryomyces hansenii CBS767: 6318Apis mellifera: 6292Kluyveromyces lactis NRRL Y-1140: 5327Candida glabrata CBS138: 5181Schizosaccharomyces pombe 972h-: 5035Eremothecium gossypii: 4718Theileria parva: 4079Xenopus tropicalis: 4069Cryptosporidium hominis: 3886Cryptosporidium parvum: 3396Sus scrofa: 938Trypanosoma brucei: 599Ovis aries: 253Strongylocentrotus purpuratus: 215Felis catus: 162Plasmodium yoelii yoelii: 105Takifugu rubripes: 7Ciona intestinalis: 3Trypanosoma cruzi: 3

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Genome Annotation in Entrez Nucleotide

GenBank Components (clones, WGS) NT/NW Contigs NC

Assembly

Components

Genome

Components

NM/XMMaster

mRNA

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Genome Annotation Links

curated mRNA

genomic contig on human chromosome 2containing NM_000547

human chromosome 2

the 21 contigs of the chromosome 2 assembly

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Getting the Annotation Details

Genomic sequence

ACCESSION NC_000002 REGION: 1396242..1525502

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Getting the Annotation Details

exon-intron structure

These flat files contain all annotations in the gene and the full, explicit sequence

ACCESSION NC_000002 REGION: 1396242..1525502

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Searching Entrez Gene

RefSeq status and variants: Reviewed RefSeqs with transcript variants

srcdb refseq reviewed[prop] AND has transcript variants[prop]

Gene symbol: human thyroid peroxidase (TPO)

tpo [sym] AND human [organism]

Disease and Gene Ontology: Membrane proteins linked to cancer

integral to plasma membrane[gene ontology] AND cancer [dis]

Chromosome and Links: genes on human chromosome 2 with OMIM links

2 [chromosome] AND gene omim [filter] AND human [organism]

Protein name: topoisomerase genes from Archaea

topoisomerase[gene/protein name] AND archaea [organism]

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Gene Links in Entrez

Microarray datasets for TPO

Gene homologs for TPO

DNA and RNA sequences for TPO

Phenotypes involving TPO

Protein sequences for TPO

Literature abstracts about TPO

Sequence polymorphisms in TPO

Species whose genome has this TPO gene

STS markers in the TPO gene

ESTs aligned to the TPO gene

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Examples of sequences appropriate for TPA are:

Annotation of features on gene and/or mRNA sequences

Assembled “full length” genes and/or mRNAs

NCBI now accepts the submission of new annotationsof existing GenBank sequences.

• Submissions must be published in a peer-reviewed journal.

• Facilitates the annotation of sequences by experts.

What should not be submitted to TPA?

Synthetic constructs (such as cloning vectors) that use well-characterized, publicly available genes, promoters, or terminators

Updates or changes to existing sequence data

Sequence annotations without experimental evidence

Third Party Annotation(TPA) Database

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Beyond RefSeq

If your organism does not have RefSeqs…

• UniGene : gene-based clusters of cDNAs and ESTs

• WGS sequences in Entrez Nucleotide (wgs[prop])

• Trace Archive

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A gene-oriented view of sequence entries

•MegaBlast based automated sequence clustering

•Now informed by genome hits New!

•Nonredundant set of gene oriented clusters

•Each cluster a unique gene

•Information on tissue types and map locations

•Includes known genes and uncharacterized ESTs

•Useful for gene discovery and selection of

mapping reagents

What is UniGene?

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Organisms in UniGene Top Ten1. Human2. Rice3. Mouse4. Cow5. Wheat6. Zebrafish7. Pig8. Chicken9. Frog (X. laevis)10. Frog (X. tropicalis)

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Finding UniGene Clusters

by link

by Entrez search

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UniGene Cluster for TPO

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GPLPlatform

descriptions

GSMRaw/processedspot intensities

from a singleslide/chip

GSEGrouping of

slide/chip data“a single experiment”

GDSGrouping ofexperiments

Curated byNCBI

Submitted byExperimentalistsSubmitted by

Manufacturer*

Entrez GEOEntrez

GEO Datasets

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Linking to GEO

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GEO Datasets

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Whole Genome Shotgun Projects

• Traditional GenBank Divisions• 300 + projects

– Viruses– Bacteria– Environmental sequences– Archaea– 73 Eukaryotes featuring:

• Cow, Chicken, Rat, Mouse, Dog, Chimpanzee, Human • Pufferfish (2), Zebrafish• Honeybee, Anopheles, Fruit Flies (4), Silkworm• Nematode (C. briggsae)• Yeasts (9), Aspergillus (3)• Rice

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Trace Archive

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Short-tailed opossum traces

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Viewing Simple Genomes

• Full chromosomal sequences are provided

• Genes are annotated

• The annotation can be shown graphically and linked to sequence records

All are RefSeq NC records in Entrez Genome

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mutL

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Viewing Complex Genomes

• Map Viewer Home Page– Shows all supported organisms– Provides links to genomic BLAST

• Genome Overview Page– Provides links to individual chromosomes– Shows hits on a genome graphically

• Chromosome Viewing Page– Allows interactive views of annotation details– Provides numerous maps unique to each genome

NCBI Map Viewer

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eMap Viewer Home Page

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Genome Overview Page

Genomic BLAST

Species-specific help!

Search the maps

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Chromosome Viewing Page

Master Mapwith exploded content

Genes

UniGene

Contigs

Ideogram

Add or remove maps

ZoomingControls

Map Summary

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eMap Summary

TPO’s contig!

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Map ContentMap content varies greatly by species!

• Sequence Maps• Core assembly• Annotation evidence• Clones & Markers• Polymorphisms• Links & Features

• Genetic Maps• Cytogenetic maps• Linkage maps• Radiation hybrid maps

AssemblyContigComponentTranscriptGene

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View the Assembly near TPO

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eAssembly of Chr. 2

NT_033000

1255072

1563756

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Assembly of Chromosome 2

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eZooming

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eView of TPO

Links to Entrez Gene

Links to Entrez Nucleotide

Links to Tools and Data

Gap in assembly

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Map ContentMap content varies greatly by species!

• Sequence Maps• Core assembly• Annotation evidence• Clones & Markers• Polymorphisms• Links & Features

• Genetic Maps• Cytogenetic maps• Linkage maps• Radiation hybrid maps

Ab initio (model)GenBank DNAESTUniGeneGene

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Annotation Evidence

Ab initio models

UniGene Clusters

Aligned ESTs

GenBank records not used in assembly

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eEntrez Homologene

Homologs by protein BLAST