PubMed Nucleotide Protein Genome Structure Taxonomy

Entrez Map Viewer Help Document Revised 10/26/00

  1. Overview
  2. Organisms Represented in the Entrez Map Viewer
  3. Genome-Wide Search
  4. Chromosome-Specific Search
  5. Links to Related Data
  6. Sequence View
  7. Constructing URLs to Map Search and Map Viewer
Overview back to top

Entrez Genomes presents a unified graphical view of maps (genetic and physical) and sequence data for a selected organism.

The Entrez Map Viewer, described in this document, is a software component of Entrez Genomes. It allows you to view an organism's complete genome, integrated maps (when available) for each chromosome, and sequence data for a region of interest.

The Map Viewer works best with the most recent versions of Netscape and Internet Explorer (IE). On the PC, it is backwards compatible to Netscape and IE version 3. Backwards compatibility is not guaranteed for the Macintosh platform.

Displays are provided at four levels of detail:
  1. Home Page for an organism - summarizes the resources available for that organism
  2. Genome View - graphically displays the complete genome as a set of chromosome ideograms (to scale) and allows you to search for terms across the genome, showing the location of the hits on the chromosome ideograms
  3. Map View - presents one or more maps of interest for a selected chromosome, aligned to a Master Map that you select, and allows you to view regions of interest at different levels of resolution
  4. Sequence View - displays the sequence data for a specific chromosomal region, and graphically depicts the biological features that have been annotated on that region

You can search for a term, such as a gene symbol, across the whole genome or on a specific chromosome. If you start with a genome-wide search, the Entrez Map Viewer presents a graphic Genome View of search results. This shows the location of your gene(s) of interest with red marks on the chromosome ideograms, followed by summary information in tabular format. Using the tabular summary, you can link from a map element to a detailed Map View of the corresponding genomic region, and then zoom into progressively more detailed views. A chromosome-specific search takes you immediately to the Map View.

If multiple maps exist for a chromosome, the Map Viewer allows you to display one or more maps of interest, and to select a Master Map for which descriptive text is displayed. The maps are aligned from right (where the Master Map is shown) to left. The alignment is based on common or corresponding objects as described under "show connections," or on a conversion of estimated base pairs to cytogenetic position for the alignment of sequence maps to cytogenetic maps, and vice versa. The sequence map for a region links to a Sequence View of the corresponding nucleotides, including a graphical display of the biological features that have been annotated on that region.

It is also possible to search by map position. This can be done from the Map View of a chromosome, by (1) entering a range of interest in the side bar (in base pairs, cytogenetic bands, or between two gene symbols), (2) clicking on the region of interest in the chromosome thumbnail graphic in the sidebar, or (3) clicking on a region of interest in the enlarged Map View of the chromosome.

Examples of questions that can be answered with the Entrez Map Viewer:
  • Where does gene X exist within the genome of organism Y? What are some flanking markers?
  • Which genes exist on a chromosome, and in what order do they appear?
  • Show the genes that exist in region R of the chromosome. Show me the corresponding sequence data for that region.
  • Display the region of a chromosome between points A and B. Show both the cytogenetic and sequence map for that region, aligned to each other based on markers that have been placed on both maps.
  • What is the distance between two genes? (Note: scale depends on the type of map on which those genes have been placed.)
  • I know the cytogenetic location of gene X. What is the corresponding physical location?

Organisms Represented in the Entrez Map Viewer back to top

This help document describes the general features of the Entrez Map Viewer.

However, the number and types of maps displayed by the Map Viewer vary by organism. The types of searchable terms also vary by organism.

Additional details, such as descriptions of available maps, are provided for each organism currently represented in the Entrez Map Viewer:

Entrez Genomes provides access to over 800 complete genomes, and the Map Viewer described here provides special browsing capabilities (e.g., integrated maps) for the organisms noted above. For the other organisms, Entrez Genomes also provides graphical overviews of complete genomes/chromosomes, and the ability to explore regions of interest in progressively greater detail. A brief description of Entrez Genomes is provided in the NCBI Site Map. The Genomes and Maps section of the Site Map provides additional information available for specific genomes.

Genome-Wide Search back to top

Access Points back to top

You can search across a whole genome from that organism's Genome View page. It shows a graphic of all the chromosomes (to scale), and allows you search both cytogenetic and sequence data. Sequence data not yet placed on a chromosome is represented by a "not-placed" icon.
Drosophila melanogaster genome view
Homo sapiens genome view
Mus musculus genome view

Query Input back to top

Searchable Terms

The search bar near the top of the page allows you to enter a term, such as a gene symbol or marker name. The chromosome number search field is optional, as described below.

The types of terms that can be used for searching vary by organism. Some types of terms are generally searchable in all genomes, such as:

  • gene symbol
  • gene name
  • marker name
  • aliases for marker name
  • text word (e.g, actin) or phrase (e.g., cell adhesion) - see details below
The search program looks for the query term in all of the maps available for an organism. For additional detail, see the section on Organisms Represented in the Entrez Map Viewer.

Truncation and Wildcards - Terms can be entered in their entirety or truncated by using wildcards:
  • Full Spelling -
    a Drosophila genome-wide search for the gene symbol "popeye" (without the quotes) will retrieve records that have an exact character string match.

  • Truncation using asterisk (*) as a wildcard -
    An asterisk can be used to represent any number of characters.
    E.g., a search for "po*" (without the quotes) will retrieve terms that begin with "po", and end with zero or more other characters.

  • Truncation using question mark (?) as a wildcard -
    A question mark represents any single character.
    E.g., a search for "h?g" (without the quotes) will retrieve terms that contain H in the first position, any character in the second p osition, and G in the third position.

  • Using both question mark (?) and asterisk (*) -
    E.g., a search for "?s*" (without the quotes) will return terms that contain any character in the first position, S in the second position, followed by any number of other characters.

Text Words and Phrases - Searches for text words (e.g., actin) or phrases (e.g., cell adhesion, integrin binding) can also be done:
  • At the present time, the words should be surrounded by asterisks. That will retrieve records with the term(s) in any position within a phrase.
  • Searching for multiple terms: if asterisks are placed only at the ends of a phrase (e.g., *cell adhesion*), the system will only retrieve records in which the terms are adjacent to each other. You can also place an asterisk between the terms (e.g., *cell*adhesion*) in order to retrieve records that contain both terms adjacent to, or apart from, each other.
  • The use of asterisks around words is a temporary measure until the text searching function is enhanced.
  • Future plans also include the implementation of Boolean operators (AND, OR, NOT) in text word searches

The Chromosome Number search field is optional:

  • no chromosome number -
    If no chromosome number is specified, all of the chromosomes for that organism are searched, as well as the genomic sequences that have not yet been placed onto a chromosome.

  • single chromosome number -
    To limit search results to a single chromosome, just enter that chromosome number into the "On Chromosome(s)" text box. Use upper case letters for X and Y chromosomes.

  • multiple chromosomes -
    To search multiple chromosomes, separate the chromosome numbers by commas (e.g., 1,3,Y)

  • range of chromosome numbers -
    Use the dash to represent a range of numbers (e.g.,   3-5    searches chromosomes 3, 4, and 5).
    To search chromosome n and higher, use a dash (e.g.,   2-   searches chromosomes 2, 3, 4...Y).

Search Output:  Genome View back to top

A genome-wide search shows the location of your search term with a red mark on the appropriate chromosome ideogram. The chromosome numbers are shown in blue beneath the ideograms. The number of hits on a chromosome is indicated in red, beneath the chromosome number. If the search term exists on a sequence with unknown chromosomal location, the number of matches to the term are indicated below the words "not placed."

A tabular display that summarizes information about each match to your query term is presented below the genome graphic. This table includes:

  • chromosome number (if known)
  • map element (such as gene symbol or marker name) - linked to a graphic view of that element on the chromosome map
  • map name(s) - indicating the map(s) on which the element was found

In addition, a variety of links to related resources for that map element are displayed (see Links to Related Data).

Chromosome-Specific Search back to top

Access Points back to top

There are several ways to access a chromosome view. Links to chromosome views are present:
  1. on the organism's home page (Drosophila,  human)
  2. on the organism's Genome View page
    (Drosophila melanogaster,  Homo sapiens,  Mus musculus)
  3. from LocusLink search results

Query Input back to top

Search for Terms

While viewing a chromosome, you can search for terms such as gene symbol. The types of terms that can be used for searching vary by organism. The tips described in the Searchable Terms section of the Genome-Wide search, above, also apply to the Chromosome-Specific search. Information about truncation is provided there as well.

The search bar also allows you to specify a chromosome number(s), if desired. If no chromosome number is entered into the text box, the whole genome will be searched. If you would like to limit the search to a specific chromosome, or set of chromosomes, follow the search tips given above.

If the search term exists on the current chromosome, a Map View will be shown of the appropriate region.

If the search term exists on another chromosome(s), the Genome View will be shown, indicating the chromosome(s) on which your term exists (with red marks). From the Genome View, click on the map element of interest to see its detailed Map View.

Search by Position

There are three main ways to search by map position from the Map View of a chromosome:
  1. enter a range of interest in the Region text boxes in side bar. The types of locations that can be entered (e.g., base pairs, cytogenetic bands, gene symbols) might vary by organism.
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

Search Output:  Map View back to top

The top of a Map View shows the organism name, the available set of chromosomes for that organism, the query term, and maps with matches to the query term (if a query has been performed). The organism name leads back to the home page for that organism, and the chromosome currently being displayed is indicated among the available set.

The area below shows the name of the Master Map (the active map for which text descriptors are displayed), provides a link to the Display Settings dialog box where you can customize your view, and summarizes information about the Master Map such as the number of markers on the map, and the number shown in the current view.

Customizing the Display back to top

Display Settings dialog box

The "Display Settings" link opens a new window with a dialog box that allows you to:

  • Display one or more maps
    The Map View page allows you to display one or more maps that have been aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. The maps can be shown with or without their corresponding "rulers."

    The number and types of maps vary by organism. For additional detail, see the section on Organisms Represented in the Entrez Map Viewer. Types of maps might include:

    • cytogenetic map (banding pattern); also referred to as ideogram
    • genetic linkage map (centiMorgans; cM)
    • radiation hybrid map (centiRays; cR)
    • sequence map (megabases; Mb)

    If multiple maps are displayed, they are aligned to each other from right (where the Master Map is shown) to left. The alignment is based on common or corresponding objects as described under "show connections," or on a conversion of estimated base pairs to cytogenetic position for the alignment of sequence maps to cytogenetic maps, and vice versa.

    Note:  In addition to the maps displayed for an organism in the Entrez Map Viewer, NCBI might also have other mapping information resources of interest. For example, a comparative Human/Mouse Homology Map is not displayed in the Entrez Map Viewer, but is available for your use. The NCBI Site Map lists a number of resources for various organisms in the Genomes and Maps section.

  • Select a "Master Map"
    The Map View page emphasizes a "Master Map" of your choice and makes its corresponding descriptive information visible. The master map is shown at the right edge of the display along with its details and descriptive text. The identity of the master map can be easily changed using the Display Settings dialog box. Another way to change the Master Map is to click on the right-arrow above the map of interest in the chromosome display. That will move the map to the right side of the window, where the corresponding text will also be displayed.

  • Add or Delete Maps
    The view of a chromosome generally shows only a representative subset of the maps available for an organism. To add one or more maps, open the Display Settings dialog box and select the maps of interest from the pop-up menus. To delete a map from the display, change the pop-up menu so it no longer shows the map's name, and instead simply shows the "---Select Map---" header. Another way to delete a map is to click on the above the map of interest in the chromosome display.

  • Select a region to be displayed
    Region boundaries that can be entered include gene symbols, base pairs, and cytogenetic bands.

  • Modify Page Size
    By default, 20 lines of text are shown.

  • Show Connections
    The "Show Connections" option draws lines between common points on the various maps, when two or more maps are displayed.

    Connections are made between the same objects on different maps, such as:
    1. between STSs on various maps (connections are made even when a given marker has alternate names on different maps)
    2. between genes on sequence and cytogenetic maps
    3. between several specific pairs of maps (e.g., for human, connections are drawn between the genes <-> morbid maps)

    If a marker has alternate names on different maps, "Show Connections" will link the two maps at that point, despite the differences in the marker name. For example, the marker SHGC-33169 is also known by seven other names (SGC33169, WIAF-984, RH50464, stSG23113, RH64431, RH32668, EST113499), because different mapping centers and databases often have their own naming conventions. If you search for "SHGC-33169" on the human genome view page, the system will find that marker on the WI-RH, NCBI_RH, GM99-GB4, and GM99-G3 maps. If you display these maps together and use the "Show Connections" option, lines will be drawn between the various maps on which that marker occurs, even though each map uses its own name for that marker.

    Note: There are no connections between sequence maps. Since all sequence maps are on the same coodinates, and therefore show the same region, there would be connections for all elements and they would always be horizontal.

    Also, we have not yet calculated the direct correspondence between the human Contig Map and the non-sequence maps. (A complete list of human maps is provided in the Homo sapiens genome data and search tips document.) However, the MapViewer can draw these correspondences on the fly using the human STS Map as intermediate. For example, to see the correspondence between the genomic sequences on the human Contig Map and the markers on the Genethon map, place the STS map between them using the Display Settings dialog box. There will be connections between the Genethon and STS map, and between the STS and Contig map (because the latter two use the same basepair coordinates).

  • Verbose mode
    Verbose mode displays additional descriptive text for the Master Map.

Sidebar Controls

  • Zoom Box
    The zoom box allows you to select progressively more detailed views.

  • Chromosome Thumbnail
    The chromosome thumbnail graphic highlights the region currently being displayed. The thumbnail is clickable, allowing you to jump from the current region being displayed to a new area of interest anywhere on the chromosome.

Controls built into the Chromosome Display

In addition to the display settings dialog box and the sidebar controls, there are some controls built right into the graphic display of a chromosome, including:

  •     deletes map from display (map can be added back using Display Settings dialog box)
  •     moves map to the right, so it becomes the Master Map
  •   scrolls up the chromosome
  •   scrolls down the chromosome
  • map graphics are clickable - just as the chromosome thumbnail is clickable, the enlarged map views are clickable as well, and allow you to either zoom into a more detailed view of an area, or show the sequence data for that region.

Links to Related Data back to top

Whether you do a genome-wide or chromosome-specific search, each map element displayed in your search results will be associated with a number of links (when available) that lead to additional information. The links include:

Linked Text Link Action Description

Map element Map View The results of a genome-wide search list the map elements that contain your search term. They can be from one or more maps. Following the link for a particular map element leads to a graphical Map View of the chromosomal region that contains the element. The Master Map shown in that view will vary, reflecting the map on which a particular element was placed.

Nucleotide:
sv Sequence Viewer Graphically shows the position of the map element within the sequence region. The display includes a graphic depiction of the coding region (CDS), RNA, and gene features that have been annotated on that sequence region. A 2 Kb section of sequence is shown below that, with corresponding graphic annotations of the features. The left and right arrows at either end of the sequence data allow you to move upstream and downstream.
gb GenBank view of record Displays the flat file format of the complete sequence record that contains the map element. The Features field of the sequence record shows the location of the element of interest within the reported sequence, as well as other elements annotated on that sequence.
gr GenBank view of region Displays a flat file record showing only the nucleotide sequence associated with the map element of interest. The accession number shown will be the same as in the GenBank view of the complete record (gb view, above), but only a fragment of data from the original accession is displayed, containing only the region of interest.
fr FASTA format of region Displays a FASTA formatted version of the same nucleotide sequence shown in the gr view (above), i.e., only the region of sequence data associated with the map element of interest.

Protein:
gp GenPept view Displays a GenPept flat file view of the conceptual amino acid translation for the map element of interest.
fp FASTA protein format Displays the FASTA formatted version of the protein sequence shown in the gp view (above), i.e., the gene product for the map element of interest.

Resources:
av AceView
human only

AceView provides graphical displays of gene models on genomic contigs assembled from finished and draft human high-throughput genomic sequence.

In addition to showing the predicted exon/intron structure of genes, AceView also shows the evidence supporting the models, including EST and RefSeq and other mRNA alignments and protein BLAST hits to the genomic sequence.

b Precomputed BLAST
(Drosophila only)
Displays a list of similar protein sequences from a BLAST search of the map element's gene product against the protein non-redundant (nr) database. This provides a fast way to retrieve similar proteins. Note that more protein sequences might have been added to the nr database after the blastp search was executed. Therefore, if a protein is of particular interest, you might want to BLAST it against the most recent version of the nr database.
ll LocusLink Leads to a summary of locus-specific information in the LocusLink resource. When viewing the LocusLink brief report, click on a LocusID number to see a detailed report for that locus, including official nomenclature and alternate symbols, map information, sequence data, and links to related resources.

Organism Specific Links to External Resources:
fb FlyBase Leads to the FlyBase Report for a map element, which includes cross-references to genome annotation data and homologs in other organisms.
gf GadFly Leads to the Genome Annotation Database of FlyBase (GadFly), which provides information about gene position and length, translation length, product, and function (known or hypothetical)

Sequence View back to top

There are two main ways to access the Sequence View of a chromosomal region:
  1. Genome View

    • From the genome-wide search output, follow the SV link in the tabular summary of search results that is presented beneath the chromosome ideograms.

  2. Map View

    • From the detailed Map View of a chromosomal region, follow the SV link beside the map element of interest.

    • While viewing a sequence map, click on a region of interest to open a dialog box that allows you to either "zoom in" or "show sequence." Select the latter.

The Sequence Viewer graphically shows the position of the map element within the sequence region. The display includes a graphic depiction of the coding region (CDS), RNA, and gene features that have been annotated on that sequence region. A 2 Kb section of sequence is shown below that, with corresponding graphic annotations of the features. The left and right arrows at either end of the sequence data allow you to move upstream and downstream.

Constructing URLs to Map Search and Map Viewer back to top

Connecting to Map Search back to top

URLs to search for mapped objects in a genomic context are constructed by combining these rules:

genome rule
D. melanogaster http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_srch?chr=dmchr.inf
H. sapiens http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=hum_chr.inf
M. musculus http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=mouse_chr.inf


with the options query and/or qchr, where
query is the query term (and allows * as wild card) and
qchr is an optional chromosome.

Examples:
  1. Finding where tyrosine kinases have been mapped in mouse (Note the use of the * wild card and the omission of qchr.):
    http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=mouse_chr.inf&query=*tyrosine*kinase*
  2. Finding what is mapped to human chromosome 7 that is leukemia-related (Note the use of * as wild card and 7 as the value for qchr to limit the results to chromosome 7):
    http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=hum_chr.inf&query=*leukemia*&qchr=7
  3. Finding known receptors in Drosophila:
    http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_srch?chr=dmchr.inf&query=*receptor*
Connecting to Map Viewer back to top

URLs to display a mapped object in a genomic context are constructed by combining this rule

http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/maps.cgi?

with the following options. The org and chr options are required.
(Representative URLs are below):

type URL option genome URL values
species org fly dro
human hum
mouse mou
chromosome chr all 1..n,X,Y
maps=value{[range]}{-r}{,list of map values, in left to right order of display, with the last value being the master} (where {} denotes optional qualifiers)
map name maps fly scfs, genbank, genseq, gencyto, cyto
human clone, cntg, comp, loc, snp, sts, ideogr,fish,gene,mit,morbid,thon,marsh, g3 ,gb4, rh, shgcg3, wirh, wiyac
mouse genet
maps qualifier: range   all '[' term [ ':' term ] ']', where term may be map object or coordinant value or valid cytogenetic position
maps qualifier: ruler
  all -r
number of lines in display size all 20 is the default
type of description of a mapped object verbose all on | off
show connections bewteen mapped objects links all on | off
text query query all word1+word2+word3+wordn
range of display around a map object zoom all number (% of total)
search sts by the UniSTS id sts any STS map id


Names and types of maps in MapViewer

genome URL option name displayed map coordinates
fly scfs Scaffolds sequence
genbank GenBank sequence
genseq Genes_seq sequence
gencyto Genes_cyto cytogenetic
cyto Cytogenetic cytogenetic
human clone Clone sequence
cntg Contig sequence
comp GenBank sequence
loc Genes_seq sequence
snp Variation sequence
sts STS sequence
ideogr Ideogram cytogenetic
fish FISH_Clones cytogenetic
gene Genes_cyto cytogenetic
mit Mitelman cytogenetic
thon Genethon cM
marsh Marshfield cM
g3 GM99_G3 cR10000
gb4 GM99_GB4 cR4000
rh NCBI_RH cR10000
shgcg3 Standford_G3 cR10000
wirh WI_RH cR4000
wiyac WI_YAC cR4000
mouse genet Genetic MGD genetic map

Examples of range qualifiers

range type examples
cytogenetic All the following are valid
  • [9p23-p11]
  • [9p23:9p11]
  • [9p23-p22:9p12-p11]
  • [9p23:9p12-p11]
  • [9p23-p22:9p11]
  • [9p23]
  • [84B1-84B5]
  • [84B1:84B5]
    Note: you may omit chromosome name after '-', but not after ':'.
  • any named object To show the region between mapped objects:
  • [D7S726:D7S2667]
  • [OSM:DRG1]


  • Sample URLs
    1. Find the neighborhood of a gene (query=HIRA) on all gene-containing human maps, with an ideogram (ideogr) and the sequence map as the master, in the region (zoom=2) of the HIRA gene on chromosome 22. Provide the detailed description of the genes (verbose=on). Note that the master map (loc) is the last in the list of map options (ideogr,morbid,gene,loc).
      http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/maps.cgi?org=hum&chr=22&query=HIRA&zoom=2&maps=ideogr,morbid,gene,loc&verbose=on

    2. Find FISH-mapped clones (fish) in a cytogenetic region and also on the sequence map(clone). Note that cytogenetic coordinates can be added to define a region to be retrieved and displayed.
      http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/maps.cgi?org=hum&chr=1&maps=clone,fish[1pter-p31]

    3. Show comparable regions on the Contig (cntg), GenBank(comp), Gene(gene,loc), and STS(sts) maps between the markers D7S726 and D7S2686. Show the ruler for the STS map (-r) and highlight the query terms (query-).
      http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/maps.cgi?org=hum&chr=7&maps=cntg,comp,gene,loc,sts[D7S726:D7S2686]-r&query=D7S726+D7S2686

    Questions or Comments?
    Write to the NCBI Service Desk