Tour the Human Genome with Map Viewer

NCBI is committed to an ongoing program of incorporating new data and annotation into its human genome resources and producing updated assemblies on a regular basis. The data used to generate NCBI's assembly of the human genome include draft and finished sequence deposited in GenBank by the Human Genome Project sequencing centers, as well as by individual contributors. New and updated sequence data continues to be submitted from both sources.

The Human Genome Map Viewer provides integrated access to the genome data through a collection of genetic, physical, and sequence maps. Views of the data range from specific genes to whole genomic regions of interest.

A total of 7 maps may be chosen for simultaneous display from a set of 21, including clone and FISH-mapped clone maps, several radiation hybrid maps, an EST map, and the Genethon and Marshfield genetic maps. The Map Viewer can display a particular region of the genome centered on a gene or marker of interest, or a region defined by an arbitrary base range.


Figure 1: Map Viewer display of six parallel maps for human BRCA1


Figure 1 shows six selected maps, with the display centered on the 100Kb area surrounding the BRCA2 gene. The rightmost is called the Master Map, which shows the greatest detail and provides additional links. The other maps provide summary information only.

In this example, the initial search was for the term “brca2”. Two BRCA2 records were found on chromosome 13; one for the disease associated with the gene and one for the gene itself. Following the gene link, the default display showed two maps—a sequence map labeled “Genes_seq” and a cytogenetic map labeled “Genes_ cyto”. To view the alternative set of maps shown in Figure 1, the Display Options and Zoom features were used. Each of the maps is discussed below.

The Master Map is designated by the user through the Display Options function and, in this example, it is the sequence map labelled “Genes_ seq”. The exon structure of the BRCA2 gene is shown as a set of thick lines superimposed upon the thin line that represents the entire gene.

First on the left, the Contig map shows the location of BRCA2 on a particular contig created by the NCBI genome assembly process. The entire contig may be downloaded from the map page, or viewed directly as a GenBank contig record. This contig record contains links to all features found on the contig, such as STSs, SNPs, FISH-mapped clones, annotated genes and CDSs.

Second from the left in Figure 1 is the STS map, which indicates the positions of sequence-tagged sites in the region of BRCA2. Four STS markers are shown within the range of the BRCA2 gene given on the Genes_seq map. Next, the Variation map shows many SNPs within the BRCA2 gene, with a particularly dense clustering in the region of the largest exon of BRCA2.

Figure 1 also includes two recent additions to the palette of maps available in the human Map Viewer. The EST map shows where ESTs align well to the genomic sequence, with histograms indicating the mapping density. Including links to UniGene, the EST map can be used to identify undocumented exons or to identify the prominent splice variants of genes. The GScan map shows ab initio gene models derived from GenomeScan, a program related to the popular GenScan gene prediction tool. This map includes links to the protein similarities, discovered via a blastx search of the protein databases, that were used to support the gene predictions.

Returning to the Genes_seq map, the Master Map in this example, two links to additional information are provided. The BRCA2 link leads to the corresponding Locus Link record, which provides a complete summary of information relating to the gene plus links to related resources. The “sv” link leads to the NCBI Sequence Viewer, which provides the most detailed sequence-level view of the human genome.



Figure 2: Sequence-level view of the human BRCA2 gene.


The Sequence Viewer display, a small portion of which is shown in Figure 2, shows the location of exons, CDSs, and STS markers along the BRCA2 gene. This example includes the DNA sequence for the initial region of the gene, showing the first two exons and intervening intron. One can see that the start codon is located within the second exon and that translation of this CDS indicates an initial amino acid sequence of “MPIGS...” for the BRCA2 gene product. Directly following is the STS marker sts-X95152, which is also visible on the STS map shown in Figure 1. The ends of the BRCA2 gene are marked by sts-X95152 and H48122. Note that the BRCA2 gene is encoded on the reverse complement of contig NT_009984, such that sts-X95152, which is near the beginning of the gene, is found at the bottom of the Map Viewer display. The Sequence Viewer also pin-points the location of three SNPs, two in the first intron and one in the second exon. All three SNPs are found in noncoding regions.

Any portion of the sequence shown in a Map Viewer view may be downloaded for further analysis using the Download/View feature. A tabular report for the displayed region can also be generated, including the coordinates of all Map Viewer features shown on the displayed maps, with links to each feature.

An advanced search feature is also offered. Search terms can be restricted to particular maps; specific features such STSs, clones, or contigs; certain subsets of SNPs (such as SNPs in coding vs. non-coding regions, or SNPs with various degrees of heterozygosity); or particular chromosomes. It is also possible to search for several items together so as to generate a Map View containing several features, or to search a particular region defined by a set of markers. A syntax such as “H48122 OR sts-X95157 OR brca2” will generate three hits on chromosome 13, which can be viewed together.

The latest NCBI human genome assembly can be downloaded from the Genome side of the FTP site at ftp.ncbi.nih.gov/genomes/H_sapiens.

The FTP site includes sequence data for each chromosome, as well as the mRNA and protein sequences generated by the NCBI annotation project. The data used by the Map Viewer to display the various integrated maps is contained within the “maps” sub-directory. A README file contains more details. —VP, DW

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