Chapter 20:  Using the Map Viewer to Explore Genomes

Data Sources

Non-Sequence-based Maps. Sources of maps that are not based directly on sequence include published maps in genetic, radiation hybrid, cytogenetic, and ordinal coordinate systems (where ordinal refers to clone order). The primary sources of each map are described in the online help documentation of each genome-specific Map Viewer. We are indebted to the researchers who make their mapping results so freely available. When a new version of any map becomes available, the data are also updated in the appropriate NCBI database.

Table 1

Types of Map Viewer annotation provided by NCBI

Table 1

Types of Map Viewer annotation provided by NCBI

Featurea	Coordinate systemb	Representative mapsc
STS	Sequence (Mb), Radiation hybrid (cRay), Genetic (cM), Clone content (ordinal), Cytogenetic	STS, STSnw, G3, GM4, GeneMap'99, TNG, Marshfield, Genethon, deCode, Whitehead YAC, phenotype maps such as Quantitative Trait Loci (QTL)
Clones	Sequence, Cytogenetic	Clone, BES, Components
Expression	Sequence	SAGE tag, UniGene
Genes	Sequence (Mb), Cytogenetic (band names)	Genes_seq, Genes_cyto
Gene-related	Sequence, Cytogenetic	UniGene, GenomeScan, Mitelman recurrent breakpoint, morbid
Variation	Sequence (Mb)	Variation
Published accessions	Sequence (Mb)	GenBank
Phenotype	Cytogenetic, Cytogenetic (abnormalities), Sequence	OMIM's morbid map, Mitelman's recurrent breakpoint, QTL (in progress)
Source clones	Sequence (Mb)	Component
Homology	Sequence (Mb)	Indirectly via LocusLink or UniGene. For mouse and human, through the homology (hm) link to the mouse–human homology map

a

The feature column lists the types of objects annotated on maps seen in Map Viewer. Those features in bold type are annotated on the RefSeqs; the rest are provided only from the Map Viewer, and the files are available for FTP transfer.

b

The different map types and coordinate systems that may contain a particular type of feature.

c

A partial enumeration of named maps that represents positions of this feature type.

Table 2

NCBI data resources used in NCBI-generated annotation (more...)

Table 2

NCBI data resources used in NCBI-generated annotation

Resource	Description
Clone Registry	Clone sequencing sequence status, STS content, and availability
dbSNP	Single Nucleotide Polymorphisms (SNPs), polymorphisms, small-scale insertions/deletions, polymorphic repetitive elements
Genome Guides	Directory of key resources for the genome, with links to related resources and tutorials. The directory to guide pages is available from Genomic Biology.
LocusLink	Locus-specific data for a subset of organisms with extensive links to related resources and sequence data
OMIM	Human genes and Mendelian disorders
RefSeq	NCBI's curated, non-redundant RefSeqs
UniGene	Computed clusters of cDNA and Expressed Sequence Tag (EST) sequences from the same gene, with tissue expression information and links to related resources
UniSTS	Unified, nonredundant database of sequence tagged sites (STSs)

Feature annotation is computed primarily in two ways: (1) by alignment of the defining sequence to the genome; or (2) for sequence tagged sites (STSs), by e-PCR (1). In some genomes, gene placement is based primarily on the alignment of mRNA [Expressed Sequence Tags (ESTs) and cDNAs], but only when an encoded protein is predicted. In other cases, where transcription evidence is weaker, more weight is given to identification of protein-coding regions. Gene identification is also constrained in that a known gene cannot be placed more than once in a haplotype (except for pseuodo-autosomal regions) or on an incorrect chromosome. Thus, if any reference haplotype retains inappropriately redundant sequence that encodes a gene, only one copy will be annotated as that gene. Others will be assigned interim IDs (see Chapter 14). Some ab initio methods may also be used for gene prediction. The predicted genes, as well as the mRNAs, are supplied as separate maps (gene, RNA, or GenomeScan maps).

In some cases, the position of these features may suggest the location of other genomic regions of interest. For example, the position of STS markers can help define the position of phenotypes such as quantitative trait loci (QTL). Although the best annotation of a gene or region is always through annotation by an expert researcher, automated annotation of genomes and comparison to that provided by experts can provide significant useful information. Experts interested in analyzing or assisting with genome annotation should contact us at info@ncbi.nlm.nih.gov.

Relationships among Coordinate Systems

In addition to supporting the display of multiple maps in the same coordinate system (e.g., multiple sequence-based maps), Map Viewer also displays maps in different coordinate systems by calculating the correspondances among them (e.g., sequence to genetic). This is accomplished by: (a) identifying features that have been placed on maps in different coordinate systems; and (b) using general conversion factors. In the first case, placement of STSs on the genome is critical for the integration of sequence data with other, non-sequence-based maps, such as genetic and RH maps. The integration of cytogenetic data with sequence data is achieved through alignment of sequence from clones that have been placed cytogentically, such as the human fluorescence in situ hybridization (FISH)-mapped clones from the Bacterial Artificial Chromosome (BAC) Resource Consortium (2). The integration of non-sequence-based maps with the sequence provides a powerful mechanism to access portions of sequence on the basis of marker or cytogenetic data. Many features, such as Single Nucleotide Polymorphisms (SNPs), ESTs, mRNAs, whole genome shotgun reads, and clones can be placed on the genome assembly by using standard DNA sequence alignment methods such as BLAST.

The identification of known genes within the genome assembly provides critical landmarks and functional context to the sequence data, which in turn makes it easier to traverse to other rich sources of gene and protein information, including publications, OMIM, RefSeq, Conserved Domain Database (CDD), and LocusLink.

The power of calculating correspondances between coordinate systems may be more apparent when considering a common application of Map Viewer, i.e., identifying candidate genes within a region defined by genetic markers. When markers are palced on both genetic and sequence maps, it is then possible to use the gene-related maps (gene, UniGene/EST, or ab initio predictions) to identify possible genes of interest. For more details on how to do this, see the Map Viewer Exercises in Chapter 23.

A Work in Progress

Figure 1

Evaluation of a chromosome sequence (STS) map

Figure 1

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   Evaluation of a chromosome sequence (STS) map

Potential inconsistencies in the order or orientation of sequence blocks can be investigated by displaying a genetic map (Marshfield), radiation hybrid map (TNG), and sequence map (STS) together and checking the Show connections box in the Maps & Options window. Note that some of the gray lines (connecting the same marker on different maps) are crossed, indicating that either the placement is incorrect on a map or the chromosome sequence is not ordered and oriented consistently with all map data.

Figure 2

Evaluation of gene localization and annotation

Figure 2

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   Evaluation of gene localization and annotation

A comparison of cDNA alignments (UniGene, RNA) and gene predictions (GenomeScan) to the genomic contig annotation can be achieved by displaying three maps simultaneously. The genomic contig (NT_024981.9) annotation is shown in the Genes_seq map and is displayed with the GenomeScan predictions (the GScan map) and the EST/mRNA alignments labeled by human UniGene clusters (the UniG_Hs map). Note that in this case, there are two sequence objects not included in the contig annotation: one is an ab initio prediction (the last model in the GScan map) (a); and the other is either some small gene or an alternative 3′ exon for PIK3C3 from the UniG_Hs map (b). This approach is especially useful when reviewing BLAST results in a genomic context.

1

2

For some genomes, the color-coded contig map displays whether the annotation is based on sequence assembled from draft or finished clones (blue, finished; green, whole genome shotgun; orange, draft). This is helpful when evaluating the level of confidence in the completeness of the annotation of a gene and/or its coding region.

Figure 3

Representation of ambiguity

Figure 3

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   Representation of ambiguity

(a) The marker D1S2894 is found on several maps. Note that for the first map (STS), the circle is diagonally split with two colors. The diagonal means that the marker has been placed more than once; the two colors mean that the placements are not on the same chromosome. (b) A Map Viewer display of a region of chromosome 16. SNPs that are placed more than once on the chromosome are designated by a yellow triangle. From the Contig map, it appears that at least one of these SNPs (rs3220808) is placed both on draft sequence (orange) and on finished sequence (blue). This may be an artifact resulting from misassembly or perhaps a region of segmental duplication. This diagram also illustrates the use of color to indicate the source and level of confidence in annotated genes. Blue indicates a confirmed gene with no conflicts; light green indicates EST evidence only; dark brown indicates a GenomeScan prediction with protein homology; orange means that there is a conflict between the annotated gene and the mRNA evidence. (Ab initio predictions from GenomeScan are categorized into two types, based on presence or absence of sequence similarity to vertebrate proteins or protein domains.)

Figure 3a

Figure 3b

Frequency of Updates

Although maps provided from external sources are updated when new data are available, the maps dependent on NCBI's annotation process are updated periodically in versions called “builds”. Thus, mRNA or other supporting evidence that becomes available after the data “freeze” date for one build will not be incorporated into the display until the next build. However, some of the supporting databases linked from the Map Viewer may have more updated information. For example, UniSTS may provide more recent e-PCR results, or LocusLink may show a newer name or additional sequence data. dbSNP may make major data releases between builds; in this case, the variation map is updated.

Links from NCBI Resources

Figure 4

Connecting to Map Viewer from Entrez Nucleotide, using (more...)

Figure 4

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   Connecting to Map Viewer from Entrez Nucleotide, using the Links menu in Entrez Nucleotide to connect from a record to Map Viewer

Figure 4

Figure 5

Example of a genome-specific resource page supporting (more...)

Figure 5

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   Example of a genome-specific resource page supporting queries to Map Viewer

Note that there are two ways to connect: (1) by selecting Maps from the pull-down menu in the gray bar at the top of the page and entering a query term in the Search box; or (2) by selecting a chromosome in the genome diagram on the right of the page (yellow background).

Figure 5

Sequence Similarity Searches

Figure 6

Accessing the Map Viewer display from a genome-specific (more...)

Figure 6

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   Accessing the Map Viewer display from a genome-specific BLAST results page

Selecting the Genome View button shows all of the BLAST hits on the genome.

Figure 6

Direct Query

Simple Searches

Figure 7

Representative of species-specific homepage

Figure 7

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   Representative of species-specific homepage

Note the links to the help documentation and related resources. Also note the check boxes to use the advanced query page and/or to display objects calculated to have links to any object returned by the query. A link to the genome-specific BLAST site is also provided at the top of the form.

When already at a genome-specific Map Viewer page, any combination of query terms can be entered into a Map Viewer Search for box (Figure 7). Boolean operators (AND, OR, and NOT) and the use of * as a wild card (applied to the right of any term) are supported. The Search for and Help document hyperlinks provide current details about query options. An advanced search is available for some genomes.

Queries may include any unique identifier for a database record, e.g., a sequence Accession number or OMIM (MIM) number, or a text term or phrase, e.g., a gene symbol (BRCA2) or descriptor (p53-binding), or disease name (lung cancer). The Boolean AND operator is used automatically if multiple terms are entered. Therefore, a query for “fanconi anemia” will automatically be interpreted as “fanconi AND anemia”. The wildcard operator (*) provides a convenient mechanism to retrieve genes that share a common symbol or name, as is often found for gene families. For example, a query for ABC* will return matches to the ATP-binding cassette superfamily.

The advanced query page, accessed by checking the Advanced search box, provides additional options to refine a query. These additional options, which may vary from genome to genome, are useful for restricting queries to a particular search field or map type. The advanced query page also includes predefined search options to restrict the search to data with certain properties, e.g., to only find genes associated with a known disease or with sequence variation (SNPs). Additional refinements to queries against the variation map can also be made, for example, to search for variation markers known to be in a gene or coding region.

The same options for wild cards and Boolean operators for your query term(s) apply when starting at the Map Viewer homepage. At present, however, you must select a genome to which to restrict your search. An option to query across multiple genomes is under development.

Map Viewer Summary Results

Figure 8

Map Viewer query results

Figure 8

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   Map Viewer query results

(a) Note that an OMIM (MIM) number was entered as a query, and the Show linked entries box was checked. (b) The red tick marks next to the chromosome diagram indicate where the results appear to be placed on the chromosome. The left/right placement does not indicate strand; it allows more resolution between tick marks. (c) When a result is returned as the result of a link, the data in the Match column of the table begin with linked to. The complete results for a particular chromosome can be displayed by selecting the name of the chromosome on the graphical portion of the display or selecting all matches in the summary table. The number of matches per chromosome is reported under each chromosome in the graphical overview, and the total number of results returned is indicated below that. Additional pages are provided if the query returns over 100 results. The table indicates the chromosomal location, the match found, the map element returned, the type of match found, and the specific map(s) that contains the query match. Only the first 40 characters are shown in the Match column, and therefore the portion of text that matches the query may not be displayed. All maps that contain any object are viewed by selecting the name of the object in the Map element column. To see only one map, select the name of that map. In some cases, the resultant display will contain related maps in the same sequence coordinates. For example, selecting a sequence-based gene map may result in the display of mRNA alignments, labeled with UniGene cluster designations, and ab initio predictions.

Figure 8

Viewing the Maps

The Graphical Display

Text or Position Queries

Figure 9

Representative map display

Figure 9

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   Representative map display

(a) Search and find options. (b) Compress Map allows you to select whether to display labels on maps other than the rightmost one. The Region Shown: and zoom graphic allow you to reset the range displayed either explicitly or by chromosome fractions, respectively. (c) Explanation and tools. This section reminds you of your chitin* query and provides statistics about the elements mapped on the Master Map for that chromosome. In this example, 3978 genes are annotated on chromosome IV, and 2 of 2 in the region are being displayed. The range shown is summarized, and links are provided to tools to download a region of the sequence and use ModelMaker and Evidence Viewer. The labels at the top of each map are connected to the documentation for that map, the -> makes the map become the master, and the X removes the map from the viewer. (d) Map. This section contains a representation of the order of elements in the range displayed and provides information about each, either by mousing over the label (uncompressed) or circle (compressed) of the non-master map, or by clicking on the links provided on the labels for the Master Map. This example shows that there is an option to display a ruler for any map. As described in the text and other figures, color is used in this display to convey information as well.

General information on the chromosome being viewed is summarized at the top of the map page: the species and chromosome currently being viewed, the query term, and the name of the focal map, termed the Master Map (Figure 9c).

The summary also includes the following statistics concerning the number of objects on the Master Map, which are:

• the number of objects localized (positioned) on the chromosome

• the number of objects not localized but present on the chromosome

• the number of objects localized in the region displayed (i.e., the number decreases as you zoom in)

• the number of objects for which text descriptions are shown (dependent on user-defined page length)

A thumbnail map on the left of the page provides a coarse indication of the region displayed; by default, this is a cytogenetic map, although the Master Map can be selected (Figure 9b).

Maps are displayed vertically, with the name of each map hyperlinked to a description of it (Figure 9d). Features displayed on the Master Map have brief descriptive labels; information on features on the non-Master Maps can be found by mousing over an object. The labels on the Master Map depend on the type of object and genome being explored but can provide: (a) links to resources defining the mapped element, some of which may not be at NCBI; (b) indicators of the confidence in the placement or naming or sequence in the region; (c) biological features of the element (for SNPs, this includes position in a gene or effects on the coding region); (d) direction of transcription for genes; and (e) links to tools to facilitate reviewing of the sequence (sv), downloading a subsequence of interest (seq), the mRNA alignments in a region (ev), homology maps (hm), or to create cDNA sequences in real time (mm). (See the section on Associated Tools for more information.).

Sequence (BLAST) Queries

The positions of BLAST hits are highlighted on the Contig map, and a text summary of the BLAST hit is provided with links to regional alignment reports. All of the options described previously for configuring your display are still available. Thus, it is possible to evaluate the sequence match by the location (possible intron/exon structure, percent identity) as well as to determine whether the matching genomic region contains all of the query sequence in the expected order. Adding other maps to the display using the Maps&Options window provides a powerful mechanism to determine how the query sequence corresponds to existing annotation, such as genes, gene predictions, STS markers, or SNPs. For more hints, see the tutorial section on querying the human genome by sequence.

The Tabular Display (View Data as Table/Download)

A tabular report of the region and maps being displayed can be generated by selecting the Data as Table View link (Figure 9b). The default report is restricted to 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 are in sequence coordinates, an option is presented to report data for any sequence map in the region. Note: Links are provided for downloading tab-delimited files for any or all maps.

Selecting the Region to Display

Figure 10

Representative Maps&Options window

Figure 10

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   Representative Maps&Options window

The menus and boxes in this window allow definition of the range of the chromosome to display (Region Shown:), selection of the new map(s) to add to the display (Available Maps:), establishment of the order and ruler options [Maps Displayed (left to right):], control of the display of lines connected to related objects on different maps (Show connections box), control of the length of the label on the rightmost (Master) map (Verbose Mode box), compression of the graphic (Compressed Graphics box), control of the number of labels on the Master map (Page Length: box), and control of the diagram in the Thumbnail View:. To add map(s) to the display, select the map name(s) and then click on ADD>>. To remove map(s) from the display, select the map name(s) in the Maps Displayed box and then click on <<REMOVE. Please note that this is an example of a configuration that might be useful in displaying gene-related information, i.e., maps of UniGene, Gene, and GenomeScan.

Figure 10

As the resolution of a view is changed, the chromosome diagram is updated. The view automatically centers on a highlighted query term, or on the middle of the chromosome if browsing only. The chromosome view can be moved up and down or zoomed in and out. Zooming can be achieved in several ways: (1) by using the zoom control, located in the left column; (2) by providing a range or bounding markers in the Region Shown text boxes; or (3) by selecting part of the map to display a menu with predefined zoom levels. Most menu-based zooms should be carried out in two or three steps to avoid missing the region of interest. It is also possible to scroll or reposition the display by selecting recenter from the menu that pops up when you click on the chromosome diagram at the left or on a map or by clicking on the arrows at the top and bottom of a map.

Selecting the Maps (Tracks) to Display

Maps are categorized by the coordinate system as well as type of feature. The maps available for a genome can be seen by scrolling through the Maps menu in the Maps&Options window or in the genome-specific help documentation. For display and query purposes, different types of features annotated on sequence coordinates are treated as different maps. The maps in sequence coordinates are comparable because all of the sequence maps are based on the reference to a standard genome assembly. Thus, one can display the SNP map (at high zoom level) next to the Gene, UniGene, or GenomeScan map to ascertain the number and location of polymorphisms in a region.

Some basic map controls are available directly on the display including removal of a map from the display by clicking on the X over the map and moving a secondary map to the Master Map position by clicking on the arrow next to the map label.

The Maps&Options window provides advanced options to: (a) add a ruler to any map; (b) reset the page length to display more (or less) information; (c) define region to display by providing coordinates or marker name in Region Shown boxes (also available directly on the Map Viewer display); (d) display direct connections between maps by checking the Show connections box; (e) optionally view text in Verbose or Condensed mode by selecting the checkbox. These user-defined preferences will be maintained for additional queries on different regions or chromosomes, until reset.

There has been considerable effort to integrate data on the sequence-based maps with data from non-sequence-based maps. Map connections provide a unique and powerful mechanism to identify features in a relevant region of the sequence map when starting with information from a different coordinate system (see Relationships among Coordinate Systems).

Data Access

The data displayed in Map Viewer are freely available. In addition to the view-specific reports, all of the data are available by FTP. README files document the content and format of each file. Genomic data are also available by chromosome; this includes genomic contigs (NT_ or NW_ Accession numbers) built from finished and unfinished sequence data. The contig data are available in various formats, including ASN.1, FASTA, GenBank, and GenPept. Also available in this directory are the RNAs (NM_, XM_ , and XR_ Accession numbers) and proteins (NP_, XP_).

Constructing URLs to Generate Specific Displays

Implementation

Query terms are indexed for retrieval using the Entrez system. Thus, wild cards, Boolean operators, filters, and properties are managed as for other Entrez databases.

Each distinct object on the map is assigned a unique identifier that is specific to a particular build. Each object may have other secondary identifiers, such as IDs, in the sequence, Clone Repository, dbSNP, LocusLink, UniGene, or UniSTS databases. All descriptors are indexed as text. In addition, some are indexed by specific field values or by pre-identified properties, such as genes with associated diseases, SNPs with heterozygosity values in pre-defined ranges, or evidence type for genes. These field names or properties can be applied to restrict a query either in the Web-based query form or within a URL. The complete listings of current implementations for field qualifiers and properties are provided in the online help documentation.

Data for each map are retrieved for display from a relational database based on the IDs returned from the Entrez query. The database is used only to support display; it is refreshed with each NCBI build or update of any other map but not to track changes from build to build. Data from previous builds are archived at NCBI, but direct access is not currently supported.