Factsheet: Genome Database

The Genome Database
Organism-centered listing of available genomic sequence records and projects

https://www.ncbi.nlm.nih.gov/genome
National Center for Biotechnology Information • National Library of Medicine • National Institutes of Health • Department of Health and Human Services
Scope
The Genome database at NCBI now uses a biologically-relevant schema to organize its records at the spe-
cies-level. Records from the Genome database provide summary of the organisms, genomic information of
available chromosomes and other replicons, and links to genomic sequences (in different stages of se-
quencing), their assembly, as well as annotation. Genome records also provide links to relevant entries in
the BioProject and BioSample databases, which detail the research projects and biological specimens from
which genomes were isolated and sequenced. Additionally, genome records connect to relevant records
from the Assembly database, where individual records representing different versions of genomic assemblies are availa-
ble along with download links. When relevant and available, genome records also provide links to data from sub-species,
different strains/isolates, or from different sequencing attempts.
Links to Data and Help Documents

NCBI News on the release of the current schema: https://www.ncbi.nlm.nih.gov/About/news/17Nov2011.html
Genome submission: https://www.ncbi.nlm.nih.gov/genbank/submit/
See “Genomes” and “WGS” pull-down menu
Genome browser tool: https://www.ncbi.nlm.nih.gov/genome/browse/
Genome FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/
Description of the updated genome FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/README.txt
BioProject submission site: https://submit.ncbi.nlm.nih.gov/subs/bioproject/
Requires a My NCBI login
Accessing the Data
The Genome homepage (https://www.ncbi.nlm.nih.gov/genome/) provides access to records in the database through
text searches (A) or browsing via the “Browse by Organism” link (B). A link to the genomes FTP site is available for data
downloading purpose, with the FAQ page link below (https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/) providing details
on the organism-centric and assembly-based directory structure (C). An NCBI news entry summarizing this change is
also available online at: https://www.ncbi.nlm.nih.gov/news/08-26-2014-new-genomes-FTP-live/
C E
F
D
The “Custom Resources” and “Other Resources” sections (D) provide links to other web pages and databases main-
tained by NCBI. The “Genome Tools” and “Genome Annotation and Analysis” sections (E) provide links to analysis tools
available from NCBI. The “External Resources” section (F) lists links to representative resources outside NCBI.
NCBI Handout Series | NCBI Genome | Last Updated on December 26, 2017 Contact: info@ncbi.nlm.nih.gov
Page 2 The Genome Database at NCBI
Browsing or Searching for Genome Records

The “Browse by Organism” page provides an easy way to locate a specific genome record using the text input box. The
example shows a display filtered by “pinus” (A), which retrieves three Overviews (B). The “Eukaryotes” tab provides de-
tails of projects with a summary on each assembly (C). Accession number in the Assembly column (D) links to the full
report in the Assembly database with more details on that assembly. Filters button provides preset criteria to refine large
list, and Columns button allows customization of the table display (E).
https://www.ncbi.nlm.nih.gov/genome/browse/
B A
E
D
The search box allows direct

searching with query terms, and
the example search with a ge-
neric term “rodent” retrieves al- F
E
most 50 records (E). The “Limits”
page (F) provides quick access
to a list of preset attributes for
use to restrict the search results.
The “Advanced” page (G) pro-

vides access to indexing fields
through a pull-down menu (H) as
well as terms indexed in each G
field and their record counts (in
parentheses) through the “Show
index list” link (I). The page auto-
matically enters selected terms
into the search box (J) along
with selected Boolean operators
(AND as the default). The “Edit” link
(K) activates the search box to allow
manual input. The example search K
combines search history #5
(representing “rodent”) with the J
fielded term “has annotation
[properties]” to retrieve genome rec-
ords with rodent text term as well as
feature annotation. The “Add to his-
tory” link (L), when clicked, adds a L
new entry to the history section and I
shows how many
genome records a
given query re- H
trieves.
www.ncbi.nlm.nih.gov/genome/advanced
Contact: info@ncbi.nlm.nih.gov NCBI Handout Series | NCBI Genome | Last Updated on December 26, 2017
The Genome Database at NCBI Page 3
Data Available from a Genome Record

The title of a genome record
links to its Overview display as
shown below. This display con-
tains a list of commonly used A
FTP links at the top (A) to facili-
tate data download from the re-
organized and assembly-based https://www.ncbi.nlm.nih.gov/genome/52
genomes ftp site. I
The Overview itself provides:

A brief description of the or-
ganism (B) B
A set of selected publications
(manually closed, C)
A summary table for the refer-
ence genome (D, shown in
part)
A diagram for the ideogram (E)
with each chromosome linked C
to the NCBI MapViewer display D
The accession for a chromo-
some (F) in the “Reference
genome” table links to the se-
quence of that chromosome in
the Nucleotide database to
allow more detailed examina-
tion of the annotation in sup-
ported formats.
Links to graphical presentation
of the genome through Ge-
nome Data Viewer (F) and F
BLAST search against this ge- E
nome (G)
Relevant entries from other
NCBI databases such as As- G
sembly and BioProject in the
“Related information” section (H)
h p://1.usa.gov/1GDPcy7
Display formats (I) linked at the top of the genome

record highlight other types of data available for
this genome.
NCBI Handout Series | NCBI Genome | Last Updated on December 26, 2017 Contact: info@ncbi.nlm.nih.gov
Page 4 The Genome Database at NCBI
Prokaryotic Genomes https://www.ncbi.nlm.nih.gov/genome/169

The display of prokaryotic organ-
isms’ genome records also con- A
tains a set of FTP links at the top
(A) to allow quick download of rele-
vant sequence data files. The B G
Overview display (B) below is simi-
lar to that for eukaryotic organisms.
The Dendrogram section (C) at the
end contains a BLAST-based dis-
tance tree to address the related-
ness of these strains or sub-
species and highlights the com-
plexity of this relationship, with the
reference genome marked in yel-
low (D). Clicking a node highlights
its branch (green, E). The context
menu (activated upon hovering, F)
provides functions for tree manipu-
lation and access to specific ge-
nomes under the node, organized
in a table similar to “Genome As-
sembly and Annotation re-
port” (G) .
Feedback
Please address comments and feedback to info@ncbi.nlm.nih.gov
C
Contact: info@ncbi.nlm.nih.gov NCBI Handout Series | NCBI Genome | Last Updated on December 26, 2017

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The Genome Database

Organism-centered listing of available genomic sequence records and projects

Links to Data and Help Documents

Browsing or Searching for Genome Records

The search box allows direct

The “Advanced” page (G) pro-

Data Available from a Genome Record

The Overview itself provides:

Display formats (I) linked at the top of the genome

Prokaryotic Genomes https://www.ncbi.nlm.nih.gov/genome/169

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