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PubMed | Nucleotide | Protein | Genome | Structure | Taxonomy |
Entrez Map Viewer Help Document | Revised 10/26/00 |
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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:
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Examples of questions that can be answered with the Entrez Map
Viewer:
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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:
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Access Points | ![]() |
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 |
Query Input | ![]() |
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:
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Truncation and Wildcards - Terms can be entered in their
entirety or truncated by using wildcards:
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Text Words and Phrases - Searches for text words (e.g.,
actin) or phrases (e.g., cell adhesion, integrin
binding) can also be done:
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The Chromosome Number search field is optional:
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Search Output: Genome View | ![]() |
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:
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Access Points | ![]() |
There are several ways to access a chromosome view. Links to
chromosome views are present:
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Query Input | ![]() |
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:
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Search Output: Map View | ![]() |
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 | ![]() |
Display Settings dialog box The "Display Settings" link opens a new window with a dialog box that allows you to: |
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Sidebar Controls |
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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:
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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 |
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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. |
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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. |
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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. |
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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. |
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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) |
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There are two main ways to access the Sequence View of a chromosomal
region:
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Connecting to Map Search | ![]() |
genome | rule |
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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 |
Connecting to Map Viewer | ![]() |
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 |
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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 |
genome | URL option | name displayed | map coordinates |
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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 |
range type | examples |
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cytogenetic | All the following are valid Note: you may omit chromosome name after '-', but not after ':'. |
any named object | To show the region between mapped objects: |
Questions or Comments? Write to the NCBI Service Desk |