PubMed Nucleotide Protein Genome Structure Taxonomy

Entrez Map Viewer Help Document Revised January 26, 2004

The Map Viewer provides special browsing capabilities for a subset of organisms in Entrez Genomes. The organism subset is shown below and also on the Map Viewer Home Page. Map Viewer allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. The number and types of available maps vary by organism, and are described in the "data and search tips" file for each organism. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

  1. Overview
  2. Organisms Represented in the Entrez Map Viewer
    Mammals
    Homo sapiens  (human) data and search tips search the genome
    Mus musculus  (mouse) data and search tips search the genome
    Rattus norvegicus  (rat) data and search tips search the genome
    Bos taurus  (cow) data and search tips search the genome
    Canis familiaris  (dog) data and search tips search the genome
    Sus scrofa  (pig) data and search tips search the genome
    Other Vertebrates
    Danio rerio  (zebrafish) data and search tips search the genome
    Invertebrates
    Anopheles gambiae  (mosquito) data and search tips search the genome
    Caenorhabditis elegans  (nematode)   search the genome
    Drosophila melanogaster  (fruit fly) data and search tips search the genome
    Plants
    Arabidopsis thaliana  (thale cress) data and search tips search the genome
    Avena sativa  (oat) data and search tips search the genome
    Glycine max  (soybean) data and search tips   search the genome
    Hordeum vulgare  (barley) data and search tips search the genome
    Lycopersicon esculentum  (tomato) data and search tips search the genome
    Oryza sativa  (rice) data and search tips search the genome
    Triticum aestivum  (wheat) data and search tips search the genome
    Zea mays  (corn) data and search tips search the genome
    Fungi
    Saccharomyces cerevisiae  (baker's yeast) data and search tips search the genome
    Schizosaccharomyces pombe  (fission yeast) data and search tips search the genome
    Magnaporthe grisea  (rice blast fungus) data and search tips search the genome
    Neurospora crassa  (orange bread mold) data and search tips search the genome
    Protozoa
    Plasmodium falciparum  (malaria parasite) data and search tips search the genome
  3. Search strategies
  4. Legend
  5. Sequence View
  6. Reports (Data as Table View)
  7. Constructing URLs that:
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.

Four Levels of Detail Shown Per Genome back to top

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.

Sample Questions that can be answered with Map Viewer back to top

Examples of questions that can be answered with the Entrez Map Viewer:
  1. Where does gene X exist within the genome of organism Y? What are some flanking markers?
  2. Which genes exist on a chromosome, and in what order do they appear?
  3. Show the genes that exist in region R of the chromosome. Show me the corresponding sequence data for that region.
  4. 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.
  5. What is the distance between two genes? (Note: scale depends on the type of map on which those genes have been placed.)
  6. I know the cytogenetic location of gene X. What is the corresponding physical location?

Exercises/Tutorials back to top

The NCBI Handbook includes a series of exercises that demonstrate additional questions that can be answered with Map Viewer, such as:

  1. How do I obtain the genomic sequence around my gene of interest?
  2. If I have physical and/or genetic mapping data, how do I use the Map viewer to find a candidate disease gene in that region?
  3. How can I find and display a gene with the Map Viewer?
  4. How can I analyze a gene using the Map Viewer?
  5. How can I create my own transcript models with the Map Viewer?
  6. Using the Mouse Map Viewer
  7. How can I find members of a gene family using the Map Viewer?
  8. How can I find genes encoding a protein domain using the Map Viewer?

Hardware and Software back to top

The Map Viewer works with recent versions of Netscape on Unix, and with Netscape or Internet Explorer on PCs. On the Macintosh, Map Viewer works better with Internet Explorer.

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. Therefore, a separate "data and search tips" file is provided for each organism. It provides descriptions of the available maps, and search tips, for that organism.

The organisms currently represented in the Entrez Map Viewer are shown below, and are also shown on the Map Viewer Home Page.

Mammals
Homo sapiens  (human) data and search tips search the genome
Mus musculus  (mouse) data and search tips search the genome
Rattus norvegicus  (rat) data and search tips search the genome
Bos taurus  (cow) data and search tips search the genome
Canis familiaris  (dog) data and search tips search the genome
Sus scrofa  (pig) data and search tips search the genome
Other Vertebrates
Danio rerio  (zebrafish) data and search tips search the genome
Invertebrates
Anopheles gambiae  (mosquito) data and search tips search the genome
Caenorhabditis elegans  (nematode)   search the genome
Drosophila melanogaster  (fruit fly) data and search tips search the genome
Plants
Arabidopsis thaliana  (thale cress) data and search tips search the genome
Avena sativa  (oat) data and search tips search the genome
Glycine max  (soybean) data and search tips   search the genome
Hordeum vulgare  (barley) data and search tips search the genome
Lycopersicon esculentum  (tomato) data and search tips search the genome
Oryza sativa  (rice) data and search tips search the genome
Triticum aestivum  (wheat) data and search tips search the genome
Zea mays  (corn) data and search tips search the genome
Fungi
Saccharomyces cerevisiae  (baker's yeast) data and search tips search the genome
Schizosaccharomyces pombe  (fission yeast) data and search tips search the genome
Magnaporthe grisea  (rice blast fungus) data and search tips search the genome
Neurospora crassa  (orange bread mold) data and search tips search the genome
Protozoa
Plasmodium falciparum  (malaria) data and search tips search the genome

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.

Search Strategies back to top

Genome View and Map View back to top

Query bars to interrogate Map Viewer occur in two contexts. One, called Genome View, provides an option to enter general query terms, chromosome values, and strain/haplotype names. The other, called Map View, only supports the general query box, but does provide an option to restrict a subsequent query to the region of the chromosome currently displayed, in case the object of interest is not highlighted as the result of a query.

If a search is launched from the Map View, and the result 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.

Genome View back to top

The Genome View page shows a graphic of all the chromosomes (to scale), and allows you search the data in all the maps available for that organism. The data can include a variety of maps, such as sequence, cytogenetic, genetic, radiation hybrid, and others. Sequence data not yet placed on a chromosome is represented by a "not-placed" icon.

The list of organisms represented in the Map Viewer provides links to the genome view page of each organism ("search the genome"), and to additional information about the scope of data available for each genome.

Map View back to top

The chromosome-specific view (called Map View) shows one or more detailed maps for a single chromosome (see customizing the display). It displays a list of the elements on the master map, and allows you to view the maps in progressively greater levels of detail.

Chromosome views (Map Views) can be accessed in several ways:
  1. by clicking on the chromosome number beneath its icon on an organism's genome view page (links to genome views of various organisms are provided above)
  2. by clicking on the map element name in the tabular results of a genome-wide search (described above)
  3. by clicking on the map name in the tabular results of a genome-wide search
  4. from other resources within NCBI that provide links to mapped objects, usually designated Map Viewer or mv.

Constructing Queries - General Query Text Box back to top

Searchable Terms back to top

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 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:

  • clone name
  • gene symbol
  • gene name
  • marker name
  • aliases
  • text word (e.g, actin) or phrase (e.g., cell adhesion) - see details below
  • phenotype
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 back to top

Terms can be entered in their entirety or truncated by using * as a wildcard.
  • Full Spelling -
    a genome-wide search of human for the gene symbol DIAPH1 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 at the end of a word or phrase.
    • a search for DIAPH* will retrieve records containing terms that begin with "DIAPH", and end with zero or more additional characters.
    • a search for "cell adh*" will retrieve records containing phrases that begin with "cell adh", and end with zero or more additional characters.
      Note the requirement for double quotes (") to surround the phrase.

Text Words and Phrases back to top

  • Searches for text words (e.g., actin, alzheimer) within longer terms are suppported.
  • Words can be entered in their entirety (e.g., nephropathy) or as a word stem followed by the asterisk as a truncation symbol (e.g., nephro*) and will retrieve records that contain that word or word fragment only in the context of a phrase.
    The truncation symbol can only be used on the right side of a term.
  • Searching for multiple terms: words are indexed individually and as phrases. If multiple terms are entered in the query box without quotes, a Boolean AND is assumed (e.g., a search for cell adhesion interpreted as cell AND adhesion). That means that both terms had to occur in the same record. but not necessarily next to each other. However, if double quotes are used, adjacency of the terms is required.
  • Words can be searched in all fields (default), or limited to specific fields described in the search fields section of the document on Homo sapiens genome data and search tips
  • Words can be be combined with Boolean operators (AND, OR, NOT)

Chromosome back to top

The Chromosome search field is optional and present only on the Genome View page.

  • no chromosome -
    If no chromosome 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 -
    To limit search results to a single chromosome, just enter that value 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 values by commas (e.g., 1,3,Y)

  • range of chromosomes -
    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).

Haplotype or strain back to top

Depending on the genome being queried, it may be useful to restrict the search by strain or haplotype. This search field is optional, and present only on the Genome View page.

  • no entry -
    If no strain or haplotype is specified, all are searched.

  • single value -
    To limit search results to a single strain or haplotype, enter its name in the text box labeled strain or haplotype. Right truncation is NOT currently supported in this field.

  • multiple values -
    This function is currently not supported.

Note:  For Danio rerio, please consider chromosome to signify linkage group (LG).

Search Output:  Genome View back to top

The results of a genome-wide search include two main items:
  1. a graphic of all the chromosomes (to scale), with red tick marks showing the location of markers that contained your search term
  2. a tabular summary of markers that contained your search term, and the chromosome and specific maps on which those markers are found.
Beneath each chromosome graphic, the chromosome number is shown in blue. The number of hits on a chromosome is indicated in red, under 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  (Note: if you click on the map element name, the Map Viewer will display an alignment of all the maps on which the element was found, highlighting the position of the element)
  • map name(s) - indicating the map(s) on which the element was found  (Note: if you click on a map name, the Map Viewer will display only that map, highlighting the position of the element)

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

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 Maps&Options 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. The Download/View Sequence/Evidence link allows several region-specific functions [not always available for all genomes], namely downloading the genomic sequence and using the Evidence Viewer.

Customizing the Display back to top

Search by Position back to top

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  (see details in separate help documents for Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Hordeum vulgare, Mus musculus, Oryza sativa, Rattus norvegicus, Triticum aestivum, Zea mays).
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest along the line denoting a particular map in the enlarged Map View of the chromosome

Maps & Options dialog box back to top

The Maps & Options link (originally called "Display Settings") opens a new window with a dialog box (Figure.) that allows you to:

  • Select one or more genomes from which to display comparative maps

    Map Viewer supports comparative views for an increasing number of genomes. You can use the Maps&Options interface to select what other genomes to display relative to a genome of reference, and the maps to display on all.

    If you want to change the organism or assembly for a map already in the box at the right, use your mouse to highlight the map name, select the assembly from the Assembly: menu, and click the Change Chr/Assembly button.

    If more than one genome or assembly is selected for display, map boundaries in the resultant Map View are also indicated by constrasting background colors, labeled by the name of the genome, assembly and map.

  • Select one or more assemblies or chromosomes on which to display annotation

    When different assemblies for a genome or chromosome are available, Map Viewer allows you to specify what annotation you want to see on one or more assemblies. The default is set to ref for the reference assembly. To add a map for a different assembly, make your selection from the Assembly menu, highlight the map name in the left box, click the Add button, and the map will appear in the right box with the assembly name in the second section delimited by square brackets[]. For the reference assembly, the second [] section is left empty.

    If you want to change the assembly for a map already in the box at the right, use your mouse to highlight the map name, select the assembly from the Assembly: menu, and click the Change Assembly button.

    If more than one assembly is selected for display, map boundaries in the resultant Map View are also indicated by constrasting background colors, labeled by the name of the assembly and map.

  • Display one or more maps

    The Map View page allows you to display one or more maps that have been aligned relative to each other based on objects (e.g. markers or genes), 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.

  • 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 Maps & Options dialog box and click on map(s) of that you want to add or delete to highlight them, and then click on ADD>>. To delete click on the names in the box at the right then click on REMOVE. 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 Shown)
    Region boundaries that can be entered include gene symbols, base pairs, and cytogenetic bands.

  • Modify Page Size (Page Length)
    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.

    Map Viewer can calculates correspondences between maps in different coordinate systems (e.g. genetic and sequence) on the fly based on shared objects. 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.

  • Compress Map and Auto Compress
    It is possible to remove labels from non-master maps. If auto is selected, use the Auto Compress box to set the width of the display at which you want compression to be active. The default is 350 pixels. You can also turn compression on or off completely.

Sidebar Controls back to top

  • Zoom Box
    The zoom box allows you to select progressively more detailed views. There are two zoom box styles; which one is shown depends on the organism being viewed.

In the zoom box with thick bars, the longest bar displays the full chromosome, and subsequent bars display 1/10th, 1/100th, 1/1,000th, and 1/10,000th of the chromosome, respectively.
In the zoom box with thin bars, the longest bar displays the full chromosome, and each subsequent bar zooms in by a factor of 2 (showing 1/2 of the previous length displayed).

  • 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. For some organisms (e.g., human), radio buttons beneath the thumbnail graphic allow you to select which map is displayed there:  the ideogram or the master map.

Controls built into the Chromosome Display back to top

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.

Legend 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 number and type of links depend on on which organism is viewed, and which map is displayed as the master map. The links that can appear are described below.

Verbose Mode back to top

By default, the master map at the right side of the display is shown in verbose mode, which provides descriptive information (as available) for each object on the master map.

Orientation back to top

Object Location Symbol Meaning
Plus strand Genes shown to the right of the grey line are transcribed in the + orientation (from top down); contigs with a + orientation are read from top down
Minus strand Genes shown to the left of the grey line are transcribed in the - orientation (from bottom up); contigs with a - orientation are read from bottom up
Unknown ? The orientation of the map element is unknown.

Links to Related Resources 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.

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.
pr RefSeq proteins Provides a link to Entrez Protein to view the protein(s) annotated for a gene.
dl Sequence Download
Formerly labeled seq

Opens a form that allows you to download a region of a chromosome. The form has two parts: (1) the top part allows you to enter chromosome coordinates in text boxes, and (2) the bottom part displays the NT_* contigs (or portions of them) that are found in that chromosome region.

Note that part 1 shows the position (base span) of the region on the chromosome, and part 2 shows the position of the region on the contig. The "strand" column for each contig shows whether that contig is on the plus or minus strand of the chromosome. Therefore, if a contig is on the minus strand, increasing the value of the 3' chromosome coordinate will decrease the value of the 5' contig coordinate.

The options Display and Save to Disk allow you to view the individual contigs in the region (or portions of them, depending on the chromosome region specified).

The option View Evidence provides the same functionality as the ev link adjacent to objects labeled in Map Viewer, with the difference that in this form, the range of the chromosome/contig being displayed is not limited by the span of an object, but by the span set on the form.

By default, the dl link beside each gene displays the chromosome and contig coordinates for the span of that gene. To view/save additional sequence data upstream and downstream of the gene, simply adjust the chromosome coordinates and press the "Change Region" button. Note that the contig coordinates will also change.

ev Evidence Viewer This option is not supported for all genomes. When available, it provides a graphical display of the biological evidence supporting a particular gene model. It displays all RefSeq models, GenBank mRNAs, annotated known or potential transcripts, and positions of ESTs that align to the genomic sequence region of interest. (more...)
hm HomoloGene Leads to the HomoloGene page anchored on a specific gene or model.

Some Organism Specific Links:
fb FlyBase Leads to the FlyBase Report for a map element, which includes cross-references to genome annotation data and homologs in other organisms.  (more...)
OMIM Online Mendelian Inheritance in Man Leads to an OMIM page for a map element, which includes a detailed description of the gene or disease.
MGI Mouse Genome Informatics Leads to an MGI Detail page for a map element.
RGD Rat Genome Database Leads to an RGD Gene Report page for a map element.

STS Maps Legend back to top

Colored dots indicate uniqueness of STS positions back to top

If the master map contains STSs, the righmost edge of the verbose display includes columns of colored dots that indicate which maps have data for each marker. The color of the dots indicates whether an STS has been mapped to a unique position on that map:

green dot marker has been mapped to only one location on the chromosome being displayed
green dot with black slash marker has been mapped to multiple locations on the chromosome being displayed
green and yellow dot marker has been mapped to the chromosome being displayed, and also to another chromosome
yellow dot marker has been mapped to one location, but on a different chromosome from the one being displayed
yellow dot with black slash marker has been mapped to multiple locations on a different chromosome from the one being displayed

For example, if you are viewing mouse chromosome 2, a yellow dot indicates that the map named in the column header has placed that marker in a single location on another chromosome.

Polymorphism Column back to top

The polymorphism column indicates whether the marker has been used to detect a polymorphism, with Y for yes and N for no.

Detailed Marker Information back to top

To see detailed mapping information about a marker, follow the link for that marker to its UniSTS record.

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.

Reports back to top

In addition to the data available from the ftp site, Map Viewer allows you to report all features within a region of interest as tables. This function is accessed by selecting the Data as Table View link in the blue sidebar at the left. (Handbook: Chapter 14, Figure 9b). The default report is restricted to maps and objects on those maps that were in the previous graphical display. Tables indicating the object name, or other identifier, and chromosome coordinates are provided for each map, along with many of the links seen in the graphical display. If the region being displayed on the map includes more than 1000 features per map, a warning message is displayed that points to the FTP site as an alternative for large-scale access.

If any of the maps is in sequence coordinates, an option is presented to report data for any sequence map in the region (View Data in the section called All Sequence Maps). The Download Data links are provided for downloading tab-delimited files for any or all maps.

The tabular display is generated from adding the argument &CMD=TXT to the URL for a particular MapViewer display. See the next section for more details on how to construct URLs to access Map Viewer.

Constructing URLs back to top

URLs that perform a search back to top

The basic URL for linking to the genome search page of an organism is:
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=xxxx
where xxxx is the Taxonomy ID (taxid) of the organism.  For example:
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
will display the genome search page for human.

Taxonomy IDs can be obtained from the NCBI Taxonomy Browser. A stable taxID is assigned to each node in the taxonomic tree. Note that the taxIDs below are at the species level. Although some organisms (particularly plants) are represented by multiple subspecies, the data in the Map Viewer generally represents a species overall, and do not distinguish between the various subspecies.

Taxonomy IDs for the organisms currently represented in Map Viewer are:

  Genome
TaxID
 
  Anopheles gambiae (malaria mosquito) 7165  
  Arabidopsis thaliana (thale cress) 3702  
  Avena sativa (oat) 4498  
  Bos taurus (cow) 9913  
  Caenorhabditis elegans (nematode) 6239  
  Canis familiaris (dog) 9615  
  Danio rerio (zebrafish) 7955  
  Drosophila melanogaster (fruit fly) 7227  
  Glycine max (soybean) 3847  
  Homo sapiens (human) 9606  
  Hordeum vulgare (barley) 4513  
  Lycopersicon esculentum (tomato) 4081  
  Magnaporthe grisea (rice blast fungus) 242507  
  Mus musculus (laboratory mouse) 10090  
  Neurospora crassa (orange bread mold) 5141  
  Neurospora crassa 5141  
  Oryza sativa (rice) 4530  
  Plasmodium falciparum (malaria parasite) 5833  
  Rattus norvegicus (Norway rat) 10116  
  Saccharomyces cerevisiae (baker's yeast) 4932  
  Schizosaccharomyces pombe (fission yeast) 4896  
  Sus scrofa (pig) 9823  
  Triticum aestivum (wheat) 4565  
  Zea mays (corn) 4577  
 


In addition, the following options can be added to the end of the URL. The syntax for these options is temporarily organism-dependent, as illustrated in the sample URLs below. As development of the Map Viewer continues, the method of searching will become consistent for all organisms, and will follow the rules shown for organism group A.

I.  query option can be added to search for a specific term:

More details about term searches are provided in the query input section above, especially the subsection on text words and phrases.

II.  A search can also be restricted to a particular chromosome:


Sample URLs that perform a search back to top

A.  human, mouse, Arabidopsis :
  1. Finding what is mapped to human chromosome 7 that is leukemia-related.
    Note there are two ways to limit to a specific chromosome, either using the qchr URL option, or searching for the term "7" in the chromosome field [chr]. Both ways are shown below. The term "leukemia" is not restricted to a specific search field in either of the URLs, and therefore the system searches all fields by default. The search fields available for human are described in the "data and search tips" document for that organism.
    http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606&query=leukemia&qchr=7
    OR
    http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606&query=leukemia+AND+7[chr]
  2. Finding where tyrosine kinases have been mapped in mouse:
    http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=10090&query=tyrosine+AND+kinase
  3. Finding the Arabidopsis map element that has the symbol At2g17370. Note that the search is restricted to the symbol field [sym]. Searching for the marker's alias of F5J6.1 will also work.
    http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=3702&query=At2g17370[sym]

B.  other organisms:
(Note the use of the * wild card on both sides of each search term and the use of the qchr option to specify chromosome.)
  1. Finding where tyrosine kinases have been mapped in fission yeast:
    http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=4896&query=*tyrosine*kinase*&qchr=3
  2. Finding notch-related markers/genes in Danio rerio:
    http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7955&query=*notch*
URLs that display a specific mapped object or chromosomal region back to top

URLs to display a mapped object in a genomic context, or a specific chromosomal region, are constructed by combining this rule:

http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?

with the options in the table below. The first two options, org and chr, are required, unless the query is based on a contig accession (format NT_000000). (Sample URLs are below.)


URL Options back to top

type URL option genome URL values
species taxid

   OR

org
Anopheles gambiae taxid=7165    or   org=mosquito
Arabidopsis thaliana taxid=3702    or   org=arabid
Avena sativa taxid=4498    or   org=oat
Bos taurus taxid=9913
Caenorhabditis elegans taxid=6239    or   org=celegans
Canis familiaris taxid=9615
Danio rerio taxid=7955    or   org=danio
Drosophila melanogaster taxid=7227    or   org=dro
Glycine max taxid=3847    or   org=soybean
Homo sapiens taxid=9606    or   org=human
Hordeum vulgare taxid=4513    or   org=barley
Lycopersicon esculentum taxid=4081
Magnaporthe grisea taxid=242507
Mus musculus taxid=10090    or   org=mouse
Neurospora crassa taxid=5141
Oryza sativa taxid=4530    or   org=rice
Plasmodium falciparum taxid=5833    or   org=mal
Rattus norvegicus taxid=10116    or   org=rat
Saccharomyces cerevisiae taxid=4932    or   org=scerevisiae
Schizosaccharomyces pombe taxid=4896    or   org=spombe
Sus scrofa taxid=9823
Triticum aestivum taxid=4565    or   org=wheat
Zea mays taxid=4577    or   org=corn
chromosome chr all 1..n,X,Y, IV, IB, are sample values
assembled contigs
or scaffolds
gnl human, mouse, Anopheles gambiae, Arabidopsis, Schizosaccharomyces pombe NT_123456, NW_123456, NC_123456 are sample values
Hint: for best results, use with query=NT_123456 and cmd=focus. For some organisms, such as Arabidopsis, clone name is an acceptable value. The gnl option is an alternative to the chr option.
You can also specify which map(s) to display, as well as other details that determine the amount and type of information to be shown for that map(s). The general syntax is as follows, with optional qualifiers denoted by {}:        maps=value_set {,value_set}
  • value_set is composed of:    map_name_value{[range]}{-r}
  • multiple value_sets should be separated by commas
  • value_sets should be written in left to right order of display, with the last value being the master map
  • range is valid only for the master map; any map can have the optional -r qualifier to show its ruler
  • map name maps Anopheles gambiae
    (mosquito)
    cyto, scf, cytoscf, sat, cytosat, prot
    Arabidopsis thaliana
    (thale cress)
    clone, contig, marker, gene, ugAt, estAt, ugHv, estHv, ugOs, estOs, ugTa, estTa, ugZm, estZm
    Avena sativa
    (oat)
    axh, sxw
    Caenorhabditis elegans
    (nematode)
    clone, genetic, gene
    Danio rerio
    (zebrafish)
    gat, hs, mgh, mop, snp, ln54, t51
    Drosophila melanogaster
    (fruit fly)
    scfs, genbank, genseq, gencyto, cyto
    Glycine max
    (soybean)
    comp
    Homo sapiens
    (human)
    clone, comp, cntg, cpg, fes, gbdna, hap, haplotype, genes, model, sage, sts, rna, snp, ugHs, ugMm, ugRn, ugSs, ugBt (sequence);
    ideogr, fish, genec, mit, morbid (cytogenetic);
    decode, thon, marsh (genetic);
    g3 ,gb4, rh, shgcg3, tng, wirh (RH);
    wiyac (YAC contig)
    Hordeum vulgare
    (barley)
    cons, cons2, NABGMP1, NABGMP2
    Mus musculus
    (mouse)
    ideogr, bes, cntg, comp, fes, gbdna, genes, model, estHs, ugHs, estMm, ugMm, qtl, strain, sts, rna, snp, fpc, fpcsts, mgi, wigen, rh, wiyac
    Oryza sativa
    (rice)
    hs, r, rc94, rj94, rx97, rk98, rs98, rw99, rd00
    Plasmodium falciparum
    (malaria)
    chr, comp, gene, genet, py, sts
    Rattus norvegicus
    (rat)
    bes, comp, cntg, cpg, ideogr, fhh, genes, mcw, rna, model, shr, sts, ugMm, ugRn
    Saccharomyces cerevisiae
    (baker's yeast)
    clone, gene, marker
    Schizosaccharomyces pombe
    (fission yeast)
    clone, gene, marker
    Triticum aestivum
    (wheat)
    so
    Zea mays
    (corn)
    mw99, ibm, umc98
    To display a specific chromosome region when viewing a given map, a URL can use the range brackets [], or the BEG and END options, described below. If the latter approach is chosen, it is not necessary to include both BEG and END in the URL. If either option is missing, its default value will be used.
    maps qualifier: range   all [term {: term }]
    where term may be a map object, such as a marker name or gene symbol, a coordinate value in map units, or valid cytogenetic position (more detail below). The curly brackets {} denote optional qualifiers, indicating that the range can contain either a single value, or two values separated by a colon (:).
    maps qualifier:
    begin range
    BEG all value may be a map object, such as a marker name or gene symbol, a coordinate value in map units, or valid cytogenetic position (more detail below)
    The default value for BEG is the start of the chromosome.
    maps qualifier:
    end range
    END all value may be a map object, such as a marker name or gene symbol, a coordinate value in map units, or valid cytogenetic position (more detail below)
    The default value for END is the end of the chromosome.
    maps qualifier: ruler
      all -r
    Note: if range is used, the -r must follow the range, as in genes[1M:3M]-r
    range of display around a map object zoom all number up to 100
    which represents the percent of the chromosome to be displayed; a value of 80, for example, shows you 80% of the chromosome, including the map object of interest
    abs_zoom all numerical value
    The abs_zoom (absolute zoom) option allows you to specify the exact portion of a chromosome to be displayed, with your query term in the center.

    The scale of the numerical value depends upon the master map being displayed. For example, if the master map is a sequence map, a value of 10000000 will be base pairs (it can also be written as 10M). If the master map is a genetic linkage map, a value of 50 will represent centiMorgans, etc. The abs_zoom function can be used with any map.

    For example, if your query is CFTR, the master map is a sequence map, and your absolute zoom value is 10000000, the system will show you 10 million base pairs of the chromosome, with CFTR in the center of that region.
      human see the command option, focus value, at the end of this table for another alternative that can be used to display a region around map objects
    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
    Note: The syntax for entering words is organism-dependent; see details in the query input section above, especially the subsection on text words and phrases.
    search sts by the UniSTS id sts any STS map UniSTS id number
    command cmd all UP, DN
    Scroll up or down.
    all TXT
    Displays data as a table.
    human FOCUS
    When the focus option is used, by default 80% of the display is occupied by your hits, and 10% on each end of the display shows a portion of the chromosome upstream and downstream. This command can be qualified by &fill=[n], where n is a number between 1 and 100
    Example: &cmd=focus&fill=40
    cutoff for EST displays EST human If an EST map is displayed, the EST option can control how many ESTs must be in a clusters before the label is generated. The default is 3.
    Example: &EST=5


    Names and types of maps in MapViewer back to top

    genome URL value name displayed map coordinates
    Anopheles gambiae
    (mosquito)
    cytoBandscytogenetic
    scfScaffoldssequence
    cytoscfScaffolds on Bandscytogenetic
    satSatellitessequence
    cytosatSatellites on Bandscytogenetic
    protDm (Drosophila melanogaster) Protein Alignmentsequence
    Arabidopsis thaliana
    (thale cress)
    cntgContigsequence
    cloneClonesequence
    markerMarkersequence
    geneGenesequence
    ugAtAt UniGsequence
    estAtAT ESTssequence
    ugHvHv UniGsequence
    estHvHv ESTssequence
    ugOsOs UniGsequence
    estOsOs ESTssequence
    ugTaTa UniGsequence
    estTaTa ESTssequence
    ugZmZm UniGsequence
    estZmZm ESTssequence
    Avena sativa
    (oat)
    axhAxH_92 (Avena atlantica X Avena hirtulaca)cM
    sxwSxW_00 (Avena strignosa X Avena wiestii)cM
    Caenorhabditis elegans
    (nematode)
    cloneClone 
    markerGenetic 
    geneGene 
    Danio rerio
    (zebrafish)
    gatGates et al. (GAT)cM
    hsHeat Shock (HS)cM
    mghBoston MGH Cross (MGH)cM
    mopMother of Pearl (MOP)cM
    snpSNP (variation)cM
    ln54Loeb/NIH/5000/4000 (LN54)cR5000, cR4000
    t51Goodfellow T51cR3000
    Drosophila melanogaster
    (fruit fly)
    scfsScaffoldssequence
    genbankGenBanksequence
    genseqGenes_seqsequence
    gencytoGenes_cytocytogenetic
    cytoCytogeneticcytogenetic
    Glycine max
    (soybean)
    compCompcM
    Homo sapiens
    (human)
    clone Clonesequence
    compComponentsequence
    cntgContigsequence
    cpgCpG Islandsequence
    fesFES_Clonesequence
    hapdbSNP_Haplotypesequence
    haplotypeHaplotypesequence
    gbdnaGenBank DNAsequence
    genesGenes_seqsequence
    modelAb initiosequence
    sageSAGE_tagsequence
    stsSTSsequence
    rnaTranscript (RNA)sequence
    ugHsHs_UniGenesequence
    ugMmMm_UniGenesequence
    ugRnRn_UniGenesequence
    ugSsSs_UniGenesequence
    ugBtBt_UniGenesequence
    snpVariationsequence
    ideogrIdeogramcytogenetic
    fishFISH_Clonescytogenetic
    geneGenes_cytocytogenetic
    mitMitelmancytogenetic
    morbidMorbidcytogenetic
    decodedeCODEcM
    thonGenethoncM
    marshMarshfieldcM
    g3GM99_G3cR10000
    gb4GM99_GB4cR3000
    rhNCBI_RHcR3000
    shgcg3Stanford_G3cR10000
    tngTNGcR50000
    wirhWI_RHcR3000
    wiyacWI_YACordinal units
    Hordeum vulgare
    (barley)
    consConsensuscM
    cons2Consensus 2cM
    NABGMP1North American Barley Genome Mapping Project (Steptoe X Morex map)cM
    NABGMP2North American Barley Genome Mapping Project (Harrington X TR306 map)cM
    Mus musculus
    (mouse)
    ideogrIdeogrambands
    besBES_Clonesequence
    cntgContigsequence
    compComponentsequence
    fesFES_Clonesequence
    gbdnaGenBank_DNAsequence
    genesGenes_sequencesequence
    modelAb initiosequence
    estHsHs_ESTsequence
    ugHsHs_UniGenesequence
    estMmMm_ESTsequence
    ugMmMm_UniGenesequence
    qtlQTLsequence
    strainStrainsequence
    stsSTSsequence
    rnaTranscript (RNA)sequence
    snpVariationsequence
    fpcFingerprint Clone (FPC)sequence (estimated base pairs)
    fpcstsFingerprint Clone-STS (FPC-STS)sequence (estimated base pairs)
    mgiMGI Integrated GeneticcM
    wigenWhitehead GeneticcM
    rhWhitehead/MRC RHcR3000
    wiyacWhitehead Yacordinal
    Oryza sativa
    (rice)
    hdHD (Japanese High-density)cM
    rRcM
    rc94RC94cM
    rj94RJ94cM
    rx97RX97cM
    rk98RK98cM
    rs98RS98cM
    rw99RW99cM
    rd00RD00cM
    Plasmodium falciparum
    (malaria)
    chrChromosomesequence
    compComponentsequence
    geneGenesequence
    genetNIAID GeneticcM
    pyPy proteinsequence
    stsSTSsequence
    Rattus norvegicus
    (rat)
    ideogrIdeogrambands
    besBES_Clonesequence
    compComponentsequence
    cntgContigsequence
    cpgCpG Islandsequence
    genesGenesequence
    modelAb initiosequence
    rnaTranscript (RNA)sequence
    stsSTSsequence
    ugMmMm_UniGenesequence
    ugRnRn_UniGenesequence
    fhhFHH X ACIcM
    shrSHRSP X BNcM
    mcwMCWcR3000
    Saccharomyces cerevisiae
    (baker's yeast)
    cloneClonesequence
    geneGenesequence
    markerGeneticcM
    Schizosaccharomyces pombe
    (fission yeast)
    cloneClonesequence
    geneGenesequence
    markerGeneticcM
    Triticum aestivum
    (wheat)
    soS-O (Synthetic-Opata)cM
    Zea mays
    (corn)
    mw99MW99cM
    ibmIBMcM
    umc98UMC98cM


    Examples of range qualifiers back to top

    range type examples
    cytogenetic All the following are valid:
  • [9p23-p11]
  • [9p23:9p11]
  • [9p23-p22:9p12-p11]
  • [9p23:9p12-p11]
  • [9p23-p22:9p11]
  • [9p23]
  • [22q12.1:22q13.2]
  • [84B1-84B5]
  • [84B1:84B5]
    Note: The range operator can be a dash (-) or a colon (:). You may omit the chromosome name after a dash (-), but not after colon (:).
  • numerical positions Integer units, for example:
  • [1:50]

    The range operator must be a colon (:), not a dash (-).
    It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map, such as centiMorgans (genetic map), centiRays (radiation hybrid maps), ordinal units (YAC map), or base pairs (sequence maps). The coordinates used for each type of map are given above.

    Sequence map ranges can be written as base pairs (default), Kilobases (K), or Megabases (M).  All three examples below will display the same chromosome region:
  • [12000000:15000000]
  • [12000K:15000K]
  • [12M:15M]

  • any named objectTo show the region between mapped objects:
  • [D7S726:D7S2667]
  • [OSM:DRG1]

  • URLs that report objects as tables, with options to download back to top

    If the parameter &CMD=TXT" is added to any of the URLs constructed above, the data will be reported as a table rather than as a graphical display.

    Sample URLs that perform a search back to top

    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 (genes) is the last in the list of map options (ideogr,morbid,gene,genes).
      http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=22&query=HIRA&zoom=2&maps=ideogr,morbid,gene,genes&verbose=on

    2. Find human 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/mapview/maps.cgi?taxid=9606&chr=1&maps=clone,fish[1pter-p31]

    3. Show comparable regions on the human Contig (cntg), Component (comp), Gene (gene,genes), 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/mapview/maps.cgi?taxid=9606&chr=7&maps=cntg,comp,gene,genes,sts[D7S726:D7S2686]-r&query=D7S726+D7S2686

    4. Show potential genes (RefSeqs, ESTs, ab initio models) on a human NT accession (genomic contig), with corresponding GenBank accessions used to build the contig (displayed on the Component, "comp," map) and FISH-mapped clones (on the Clone map).
      http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&gnl=NT_023567&maps=cntg-r,clone,comp,model,ugHs,genes&query=NT_023567&cmd=focus

    5. Display mouse chromosome 6 on the radiation hybrid (rh) and genetic (mgi, wigen) maps and highlight the query term (query=D6Mit113).  Zoom into 30% of the chromosome (zoom=30), with A2m in the center of that region.
      http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?org=mouse&chr=6&maps=rh,mgi,wigen&query=D6Mit113&zoom=30

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