The NCBI Map Viewer

An online tool to view sequence- and marker-based genome maps in a single display
http://www.ncbi.nlm.nih.gov/mapview/
National Center for Biotechnology Information • National Library of Medicine • National Institutes of Health • Department of Health and Human Services

Scope and access

The Map Viewer is the primary graphical display tool for genome maps for eukaryotic organisms. The Map
Viewer has the ability to search all maps for markers, display chromosome maps, and zoom in to greater
levels of detail for a region of interest. The number and types of available maps vary by organism. Maps
are aligned using shared markers and gene names, or the sequence coordinate system. Currently ge-
nomes from more than 40 eukaryotic organisms are available through the Map Viewer. The Map Viewer
homepage (www.ncbi.nlm.nih.gov/mapview/ ) is the main gateway for searching and browsing maps of all available ge-
nomes. More details on the functions and features of the Map Viewer are available in the on-line help document
(www.ncbi.nlm.nih.gov/mapview/static/MapViewerHelp.html).

Map Viewer homepage

A target genome can be queried using terms such as gene symbols, marker names, disease names, or sequence acces-
sion numbers. The organism search box provides quick access to target organism through a pull-down list (A). Alterna-
tively, available genomes can be browsed through a list of taxonomic groups (B). Clicking the header of a taxonomic
group (C) expands the section to show the organisms with available genomic maps, their current build and links to avail-
able tools (D). The Tools
Legend (E) describes
the function of each icon B F
shown on in the Tools
column and tools availa-
ble are Map Viewer A C D
search, genome BLAST,
clone finder, region- E
zoom dialog box, and
organism-specific ge-
nome resource guide.
The help document (F)
provides more details on
Map Viewer.

Map Viewer
search result
The Map Viewer dis-
plays search results in a
summary format show-
ing the matches as red
tick marks on the ideogram (G). It also N
provides key information about the ge-
nomic assembly being searched (H) I
and a link to genome BLAST page for H
sequence-based search (I). The header G
above the result list displays the com-
plete query used in the search along
with the field restrictions and Boolean
operators if applicable (J). The number K
under the chromosome (K) indicates
the hits found on that chromosome. De-
tails are displayed in a table view (L)
below, providing more details on the
type of annotation, map and assembly J
L
for each hits. A Quick Filter (M) allows
the filtering of hits so only particular fea-
ture maps desired is kept. The Ad-
vanced Search (N) provides extensive
options for framing and refining the M
search.
NCBI Handout Series | Map Viewer | Last Update December 31, 2014 Contact: [email protected]  
Page 2 NCBI MapViewer

Map Viewer Advanced Search Page

Clicking the Advanced Search
button (A) opens up a limits page
A
with functions to make a search
result more specific. It does so B E
through field restrictions for
search terms (B), limit of searches F
to particular chromosomes (C), C
genomic assemblies (D), as well
as annotation types (E) and maps
(F). Genomic assemblies can be
displayed include the reference
assembly derived from GRC as- D
sembly, and the alternate assem-
blies of the complete hydatidiform
mole (CMH) and HuRef (J.C. G
Venter) (D). Map for variations
(from dbSNP) can be filtered
based on level of heterozygosity,
relationship to a nearby gene and
available genotype data (G).

Detailed Map Viewer Display

In the search summary page, clicking on chromosome with a red “hit” in the graphical view or a link in the table view
opens a detailed interactive display. At the top is an overview indicating the query used, the annotation, and chromo-
some shown (H). The central portion of the page displays several annotated chromosomal maps whose titles are linked
to their description in the help document (I). The feature match on the maps is colored in pink along with a vertical red
highlight (J) showing the relative length and location of the feature. The right-most map is the master, “Genes_seq” in
this case, showing the most detailed annotation information (K) and a set of links to related records in other NCBI data-
bases (L). Legends for links are given in the insert. The navigational controls in the left sidebar allow for quick customiza-
tion of the display. The region of the chromosomal maps displayed can be altered using the Region Shown (M) dialog if
specific coordinates are known, while a zoom in/zoom out feature (N) changes the resolution of the current display at
preselected intervals. The red mark in the chromosomal ideogram (O) shows the relative position of the displayed re-
gion. At the top of this section, also duplicated in the upper right corner, is a Maps & Options button (P) that launches a
new window for more detailed customization of the map display.  

P
K I
M

N
J
Legends for links

Contact: [email protected] NCBI Handout Series | Map Viewer | Last Update December 31, 2014
NCBI MapViewer Page 3 

Customizing the display with Maps & Options

Clicking Maps & Options button opens
the control window (shown at right)
providing a multitude of options to
customize an existing Map Viewer
Display. Here pull-down lists allow for D E
displaying maps based on Organism
and Assembly (A), when available. A
The list of available maps for the se-
lected combination of Organism and
Assembly is shown in the box below F
G
(B). Clicking the “ +” sign (C) to the
right of a map adds it to the Track Dis- C
played list to the right (D). Conversely,
clicking the “-” sign (E) to the right of a B
map in the Track Displayed list re-
moves it. Clicking and dragging a
track up or down the list changes its
display position (F). Clicking the “R”
icon toggles on or off the ruler display,
and a map with ruler on has its icon H
colored blue (G). Checking the “Show
Connections” option (H) will connect
the matching features on adjacent
maps with grey lines. Clicking the OK I
button (I) activates the selected
changes.

Comparing different assemblies

The Map Viewer is able to display maps from different assemblies in the same browser window for side-by-side compari-
son. Maps can be selected using the Maps and Options dialog’s Organism and Assembly options. For a limited set of
organisms, this can be used to display genomic synteny. The example below shows the sytentic region around the HTT
gene regions for mouse, rat, chimpanzee, and human. The relationship between gene loci on adjacent maps are shown
by the added grey and red lines (red highlights match from a search, J) activated by the “Show Connections” option (H).

NCBI Handout Series | Map Viewer | Last Update December 31, 2014 Contact: [email protected]  
Page 4 NCBI MapViewer

Downloading Data and Sequences

Information about features displayed in the Map Viewer window can be viewed in tabular format
using the Data as Table View link (A) in the left sidebar. In display (below), annotations and nu-
cleotide sequences can be downloaded in a number of formats: the Download All (B) saves all
displayed features to a single text file; the Download Data link in each section (C) saves the A
data (gene features in this case) for the section. The Download/View Sequence/Evidence links
to a display (D), which provides
a venue to save sequence data B
for the displayed region through C
the Save to Disk option (E).

Linking into Map

Viewer through D

genome BLAST
The Map Viewer is integrated
with a wide range of NCBI re-
sources. In addition to extensive links associated with each
map (p.2), Map Viewer is also linked from records in other F
NCBI resources such as records in Gene and Nucleotide
databases, as well as genome-BLAST results. For exam-
ple, a human genome-BLAST result page contains links to E
a customized display in Map Viewer to show matches on
annotated chromosomes under a genomic context. Specifi-
cally, a summary display is available under the Human genome view link, which sums up the hits on the ideogram (F).
Clicking the chromosome opens the detailed map display (G), where alignments are shown as colored lines next to each
map (H). The color of each line acts as an indicator of the alignment score (I).

I Related NCBI resources

Gene  www.ncbi.nlm.nih.gov/gene/ 
Genome  www.ncbi.nlm.nih.gov/genome/
RefSeq  www.ncbi.nlm.nih.gov/RefSeq/ 
BLAST  blast.ncbi.nlm.nih.gov/ 
Contact: [email protected] NCBI Handout Series | Map Viewer | Last Update December 31, 2014