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

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?

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?

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

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 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.

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.

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

• 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.

• 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)

• 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).

• 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.

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.

• 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)

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, using the Evidence Viewer, and using ModelMaker.

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

• 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.

• 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.

• 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.

•     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.

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.

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

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

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.

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.