1. NCBI Molecular Biology Resources
A Field Guide
August 2-3, 2005
University of Massachusetts

2. NCBI Resources 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

3. The National Institutes of Health
Bethesda, MD

4. The 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

5. Web Access
Text
Entrez
Sequence
BLAST
Structure
VAST

6. NCBI Web Traffic
User’s per day
Christmas and New Year’s Day

7. The NCBI ftp site
30,000 files per day
620 Gigabytes per day

8. 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

9. 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
Primary databases serve as a repository of experimentalist sequences (GenBank).
Derivative databases are sources of edited/curated sequences (RefSeq…reference sequences, UniGene...genes compared to genetic loci on genomes)

10. Primary vs. Derivative DatabasesC GA
ATT GA C GA C
ATT GA
UniGene C
Algorithms
TATAGCCG
Sequencing
Centers
ACGTGC
ATTGACTA
ACGTGC
CGTGA
TTGACA
UniSTS
EST
GenBank
Updated
continually
by NCBI
STS
Updated ONLY
by submitters
RefSeq:
Annotation
Pipeline
GSS
HTG
INV
VRT
PHG
VRL
PRI
ROD
PLN
MAM
BCT
ACGTGC
RefSeq:
LocusLink and
Genomes Pipelines
Curators
TATAGCCG
AGCTCCGATA
CCGATGACAA
Labs

11. 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

12. The Entrez System: Text Searches

13. 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

14. Entrez Taxonomy
The backbone of NCBI
[organism]

15. 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

16. Entrez Nucleotide Primary Data DDBJ / EMBL / GenBank 56,865,268
Derivative Data
RefSeq ,226,084
PDB ,973
Third Party Annotation ,650
Total ,101,975

17. What 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

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

19. ftp://ftp.ncbi.nih.gov/genbank/
GenBank Releases
Release 148 June 2005
45,236,251 Records
49,398,852,122 Nucleotides
>140,000 Species
172 Gigabytes files
full release every two months
incremental and cumulative updates daily
available only through internet
GenBank, as a product, is treated like a software product with releases (full updates) every ~2 months.
Originally it was put out on CDs, but eventually became much to large to fit, so an FTP site was set up to provide access to continually updated files.
ftp://ftp.ncbi.nih.gov/genbank/

20. The Growth of GenBank Release 148: 45.2 million records
49.4 billion nucleotides
Average doubling time ≈ 14 months*
Doubling time is currently less than 1 year and still accelerating.

21. GenBank Divisions Traditional Bulk PRI (28) Primate ROD (14) Rodent
PLN (13) Plant and Fungal
BCT (10) Bacterial/Archeal
INV (7) Invertebrate
VRT (7) Other Vertebrate
VRL (4) Viral
MAM (2) Mammalian
PHG (1) Phage
SYN (1) Synthetic
UNA (1) Unannotated
Traditional
Direct Submissions (Sequin/Bankit)
Accurate (~1 error per 10,000 bp)
Well characterized
Organized by taxonomy
Bulk
EST (349) Expressed Sequence Tag
GSS (120) Genome Survey Sequence
HTG (62) High Throughput Genomic
HTC (6) High Throughput cDNA
STS (5) Sequence Tagged Site
From sequencing projects
Batch submissions (ftp/ )
Inaccurate
Poorly Characterized
Organized by sequence type

22. A Traditional GenBank Record
LOCUS AY bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
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, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:
FEATURES Location/Qualifiers
source
/organism="Malus x domestica"
/mol_type="mRNA"
/cultivar="'Law Rome'"
/db_xref="taxon:3750"
/tissue_type="peel"
gene
/gene="AFS1"
CDS
/note="terpene synthase"
/codon_start=1
/product="(E,E)-alpha-farnesene synthase"
/protein_id="AAO "
/db_xref="GI: "
/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
The Flatfile Format
Feature Table
Sequence

23. An Example Record – M17755 Field Indexed Terms
Indexing for Nucleotide UID
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 pri
srcdb genbank

24. M17755: Feature Table TPO [gene name] CDS position in bp thyroiditis
[text word]
thyroid peroxidase
[protein name]
protein
accession

25. Sequence: 99.99% Accurate The sequence itself is not indexed…
Use BLAST for that!

26. Entrez Protein GenPept (DDBJ, EMBL, GenBank) 4,444,405
RefSeq ,753,167
PIR ,395
Swiss Prot ,005
PDB ,621
PRF ,079
Third Party Annotation ,219
Total ,693,891

27. Protein Sources and Links
PIR
no mRNA!
RefSeq
 NM_000537
SWISS-PROT
no mRNA!
GenPept
 M17755

28. First seen at NCBI, not first seen at GenBank!
Sequence Revisions
First seen at NCBI, not first seen at GenBank!
Version and GI change only if the sequence changes
The accession number always retrieves the most recent version

29. Update without a Sequence Change
June 15, 1989!
GenBank came
to NCBI in 1992!

30. Update with a Sequence Change

31. GenBank File Formats ASN.1 – The Raw Data flat file XML (4 flavors)
FASTA

32. NCBI Toolbox Toolbox Sources ftp> open ftp.ncbi.nih.gov .
/************************************************************************ *
* 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 toolbox
ftp> cd ncbi_tools
ftp://ftp.ncbi.nlm.gov/toolbox/ncbi_tools

33. Text Searches in Entrez
term1 term2
If no [limit] is specified…
Organism?  [ organism ]
Journal?  [ journal ]
User compounds?  search as phrase
Author?  [author]
else [All Fields]
term1[limit] OP term2[limit] OP …
where
limit = Entrez indexing field (organism, author, …)
op = AND, OR, NOT

34. Entrez Tabs
Limits
Provides a simple form for applying commonly used Entrez limits
Allows access to the full indexing of each Entrez database
and aids in constructing complex queries
Preview/Index
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

35. Programming Entrez: E-Utilities
ESearch
Entrez query
UID list or History
ESummary
UID list or History
Document summaries
EFetch
UID list or History
Formatted data
UID list or History
ELink
UID list or History
EPost
UID list
History

36. Finding Primary Sequences
Search Entrez Nucleotide
97.9% GenBank (primary data)
2.1% RefSeq (curated data)
Possible queries we’ve seen so far…
M17755 [primary accession] TPO [gene name]
thyroid peroxidase [title] thyroiditis [text word]
Homo sapiens [organism] thyroid peroxidase [protein name]
3060 [sequence length] /04/26 [modification date]
biomol mrna [properties] gbdiv pri [properties]
srcdb genbank [properties]

37. A Starting Query 309 records 298 records
Find nucleotide records for human thyroid peroxidase
309 records
human thyroid peroxidase
(("Homo sapiens“[Organism] OR human[All Fields]) AND
thyroid peroxidase[All Fields])
Field Limit!
human[organism] AND thyroid peroxidase
298 records
("Homo sapiens“[Organism] AND thyroid peroxidase[All Fields])
11 records aren’t human sequences!!

38. Limit by Title and Database
Entrez Nucleotide
GenBank srcdb ddbj/embl/genbank[properties]
RefSeq srcdb refseq[properties]
#1: thyroid peroxidase AND human[orgn]
#2: thyroid peroxidase[title] AND human[orgn]
#3: #2 AND srcdb refseq[properties] 5
#4: #2 AND srcdb ddbj/embl/genbank[properties] 164
primary data

39. Limit by Genbank Division
EST Division gbdiv est[prop]
Primate Division gbdiv pri[prop]
#1: thyroid peroxidase AND human[orgn]
#2: thyroid peroxidase[title] AND human[orgn]
#3: #2 AND srcdb refseq[properties] 5
#4: #2 AND srcdb ddbj/embl/genbank[properties] 164
#5: #4 AND gbdiv est[prop]
#6: #4 AND gbdiv pri[prop]
traditional GenBank records

40. Limit by Biomolecule Type
Genomic DNA biomol genomic[prop]
cDNA biomol mrna[prop]
#1: thyroid peroxidase AND human[orgn]
#2: thyroid peroxidase[title] AND human[orgn]
#3: #2 AND srcdb refseq[properties] 5
#4: #2 AND srcdb ddbj/embl/genbank[properties] 164
#5: #2 AND gbdiv est[prop]
#6: #2 AND gbdiv pri[prop]
#7: #6 AND biomol genomic[prop]
#8: #6 AND biomol mrna[prop]
genomic DNA
mRNA / cDNA

41. Limit by Protein Name
thyroid peroxidase[protein name] AND human[orgn] AND
gbdiv pri[prop] AND biomol mrna[prop]
118 records [title]  4 records [protein name]

42. Entrez Document Summaries
Links menu
Click the accession to view the record
Links to other
Entrez databases
computed for M17755

43. Entrez Links for GI 4680720 Gene annotation based on M17755
Full text online articles about M17755
All polymorphisms in the TPO gene
DNA/RNA sequences similar to M17755
Graphical view of TPO gene annotation
Human phenotypes involving TPO
Microarray datasets for M17755
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

44. Viewing M17755

45. GenBank Sequences for Human TPO
Which one is the best sequence???

46. RefSeq: NCBI’s Derivative Sequence Database
RefSeq Benefits
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

47. RefSeq: NCBI’s Derivative Sequence Database
Curated transcripts and proteins
NM_  NP_123456
NR_ (non-coding RNA)
Model transcripts and proteins
XM_  XP_123456
XR_ (non-coding RNA)
Assembled Genomic Regions (contigs)
NT_ (BAC clones)
NW_ (WGS)
Other Genomic Sequence
NG_ (complex regions, pseudogenes)
NZ_ABCD (WGS)  ZP_123456
Chromosome records in Entrez Genome
NC_ (chromosome; microbial or organelle genome)
Nucleotide
Protein

48. Creating NM Records NMs must have cDNA support Genome annotation
Longest mRNA
NMs must have
cDNA support

49. NM/NP Records in Entrez
NM_000547: variant 1
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff.
The reference sequence was derived from M and AW
On Feb 25, 2003 this sequence version replaced gi:
EST that completes 3’ end
NM_175719: variant 2
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff.
The reference sequence was derived from J , AW and M
Nucleotide
Protein

50. = ! = ? Annotating the Gene RefSeq Genbank Sequences Genomic DNA
(NC, NT, NW)
Scanning....
Model mRNA (XM)
(XR)
Model protein (XP)
= !
= ?
Curated mRNA (NM)
(NR)
Curated Protein (NP)
RefSeq
Genbank
Sequences

51. Entrez Gene and RefSeq
Gene
GenBank
RefSeq
Nucleotide
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

52. Entrez Gene: RefSeq Annotations

53. NM/NP Records in Entrez Gene

54. Entrez Gene RefSeq GraphicsNM NP

55. What about LOC440844?
Entrez Gene

56. BLAST Results for XM_496543
Is there any GenBank support for this mRNA?
srcdb ddbj/embl/genbank[prop] AND biomol mrna[prop]
no full-length hit

57. The Perils of the XM
XM records are models based only on genomic sequence, and are subject
to revision or removal with each new build of that genome.
BLAST the XM against the RefSeq database to look for a replacement:
Query= gi| |ref|XM_ |
Mus musculus expressed sequence AA (AA553001), mRNA
gi| |ref|NM_ |     
Mus musculus DNA segment, Chr 4, Wayne State University 114,
expressed (D4Wsu114e), mRNA Length=1898
Score = bits (1867), Expect = 0
Identities = 1870/1871 (99%), Gaps = 0/1871 (0%) Strand=Plus/Plus

58. Eukaryotic NM/XM Records
Bos taurus:
Oryza sativa (japonica cultivar-group):
Danio rerio:
Homo sapiens:
Arabidopsis thaliana:
Mus musculus:
Rattus norvegicus:
Pan troglodytes:
Caenorhabditis elegans:
Drosophila melanogaster:
Aspergillus nidulans FGSC A4:
Gallus gallus:
Canis familiaris:
Anopheles gambiae str. PEST:
Plasmodium chabaudi:
Candida albicans SC5314:
Dictyostelium discoideum:
Ustilago maydis 521:
Plasmodium berghei:
Gibberella zeae PH-1:
Magnaporthe grisea 70-15:
Neurospora crassa:
Aspergillus fumigatus Af293:
Entamoeba histolytica HM-1:IMSS:
Cryptococcus neoformans var. neoformans JEC21: 6594
Giardia lamblia ATCC 50803:
Yarrowia lipolytica CLIB99:
Debaryomyces hansenii CBS767:
Apis mellifera:
Kluyveromyces lactis NRRL Y-1140: 5327
Candida glabrata CBS138:
Schizosaccharomyces pombe 972h-: 5035
Eremothecium gossypii:
Theileria parva:
Xenopus tropicalis:
Cryptosporidium hominis:
Cryptosporidium parvum:
Sus scrofa:
Trypanosoma brucei:
Ovis aries:
Strongylocentrotus purpuratus:
Felis catus:
Plasmodium yoelii yoelii:
Takifugu rubripes:
Ciona intestinalis:
Trypanosoma cruzi:

59. Genome Annotation in Entrez Nucleotide
GenBank Components
(clones, WGS)
NT/NW Contigs NC
Genome
Assembly
NM/XM
Master
mRNA
Components
Components

60. Genome Annotation Links
curated mRNA
genomic contig on human chromosome 2
containing NM_000547
human chromosome 2
the 21 contigs of the
chromosome 2 assembly

61. Getting the Annotation Details
Genomic sequence
ACCESSION NC_ REGION:

62. Getting the Annotation Details
ACCESSION NC_ REGION:
exon-intron structure
These flat files contain all annotations in the gene and the full, explicit sequence

63. Searching Entrez Gene Gene symbol: human thyroid peroxidase (TPO)
tpo [sym] AND human [organism]
Protein name: topoisomerase genes from Archaea
topoisomerase[gene/protein name] AND archaea [organism]
Chromosome and Links: genes on human chromosome 2 with OMIM links
2 [chromosome] AND gene omim [filter] AND human [organism]
RefSeq status and variants: Reviewed RefSeqs with transcript variants
srcdb refseq reviewed[prop] AND has transcript variants[prop]
Disease and Gene Ontology: Membrane proteins linked to cancer
integral to plasma membrane[gene ontology] AND cancer [dis]

64. 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

65. Third Party Annotation (TPA) Database
NCBI now accepts the submission of new annotations
of existing GenBank sequences.
Submissions must be published in a peer-reviewed journal.
Facilitates the annotation of sequences by experts.
Examples of sequences appropriate for TPA are:
Annotation of features on gene and/or mRNA sequences
Assembled “full length” genes and/or mRNAs
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

66. 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

67. What is UniGene? 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
Clusters of ESTs based on automatic similarity. Each cluster represents a gene.

68. Organisms in UniGene Top Ten 1. Human 2. Rice 3. Mouse 4. Cow 5. Wheat
6. Zebrafish
7. Pig
8. Chicken
9. Frog (X. laevis)
10. Frog (X. tropicalis)

69. Finding UniGene Clusters
by link
by Entrez search

70. UniGene Cluster for TPO

71. GPL GSM GSE GDS Entrez GEO Datasets Entrez GEO Submitted by
Experimentalists
Submitted by
Manufacturer*
Curated by
NCBI
GPL
Platform
descriptions
GSM
Raw/processed
spot intensities
from a single
slide/chip
GSE
Grouping of
slide/chip data
“a single experiment”
GDS
Grouping of
experiments
Entrez
GEO Datasets
Entrez GEO

72. Linking to GEO

73. GEO Datasets

74. 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
WGS- preliminary way to getting a whole genome. WGS sequences go into traditional GenBank divisions.

75. Trace Archive

76. Short-tailed opossum traces

77. Viewing Simple Genomes
All are RefSeq NC records in Entrez Genome
Full chromosomal sequences are provided
Genes are annotated
The annotation can be shown graphically and linked to sequence records

79. mutL

80. Viewing Complex Genomes
NCBI Map Viewer
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

81. Map Viewer Home Page

82. Species-specific help!
Genome Overview Page
Search the maps
Genomic BLAST
Species-specific help!

83. Chromosome Viewing Page
Map Summary
Add or remove maps
Master Map
with exploded content
Genes
UniGene
Contigs
Zooming
Controls
Ideogram

84. Map Summary
TPO’s contig!

85. Map Content Sequence Maps Genetic Maps Core assembly
Map 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
Assembly
Contig
Component
Transcript
Gene

86. View the Assembly near TPO

87. Assembly of Chr. 2
NT_033000

88. Assembly of Chromosome 2

89. Zooming

90. View of TPO Links to Entrez Nucleotide Links to Entrez Gene
Links to Tools and Data
Gap in assembly

91. Map Content Sequence Maps Genetic Maps Core assembly
Map 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 DNA
EST
UniGene
Gene

92. GenBank records not used in assembly
Annotation Evidence
GenBank records not used in assembly
UniGene Clusters
Ab initio models
Aligned ESTs

93. Entrez Homologene
Homologs by protein BLAST