In this issue

New Cn3D 4.0

SNP Population Grows

1000th Viral RefSeq Unmasked!

New Genomes in GenBank

View the Mouse Genome with Map Viewer

Mouse Genome Resources

Recent Publications

GenBank Release 131

Anopheles Gambiae Genome

Submitting Large Sequin Files

BLAST Version 2.2.4 Released



View the Mouse Genome with Map Viewer

NCBI offers access to two annotated assemblies of the mouse genome. The first is an NCBI assembly constructed from curated contigs representing finished (Phase 3) high throughput genomic sequence. The second is the Mouse Genome Sequencing Consortium’s (MGSC) whole genome shotgun assembly, based on the February 1, 2002 freeze of the data. Views of the MGSC assembly include annotations by NCBI. Combined, these data greatly facilitate the comparison of the mouse and human genomes and pave the way for the study of mouse homologues of human disease-causing genes.

The two data sets can be accessed and viewed with the Mouse Map Viewer, a Web-based, interactive, genome display tool that enables one to visualize annotated features on the assembly, such as predicted genes, sequence tagged sites (STSs), expressed sequence tags (ESTs) UniGene clusters, and single nucleotide polymorphisms (SNPs or variations).

Results of a Mouse Map Viewer search for the mouse lipoprotein lipase gene.
Click on figure to view enlarged version

Figure 1: Results of a Mouse Map Viewer search for the mouse lipoprotein lipase gene.

Queries can be made against the whole genome or an entire chromosome by supplying a gene name or symbol, accession number or any other valid numerical identifier in the textbox on the main search page. Checking the box next to the “Show linked entries” will display all of the mapped elements associated with the query term. Clicking on the chromosome of interest leads to view of a whole chromosome. The main search page also provides a link to the mouse genome BLAST pages. The BLAST results page provides a “Genome View” button that links to the Mouse Map Viewer and permits the visualization of BLAST hits in a genomic context.

A variety of maps are available for the two assemblies, including sequence-based maps, fingerprint clone data, and genetic, radiation hybrid and YAC mapping data. A total of 13 maps from a collection of 28 can be displayed in a single view. The “Maps and Options” link provides additional display options for the selected maps. By default, the selected maps are displayed from left to right, and the rightmost map, termed the “Master Map”, gives additional descriptive information about a given map element. Any map can be promoted to the Master Map by simply clicking on the arrow above the map or by choosing this feature from Maps and Options.

Some features of the Mouse Map Viewer are illustrated in Figure 1, which shows the results of a search for the gene encoding the mouse Lpl gene for lipoprotein lipase. The Lpl locus is displayed in the con-text of five different maps: Contig_ MGSCv3, Component _MGSCv3, Mm._Unigene_MGSCv3, Variation_ MGSCv3, and Gene_ MGSCv3. Lpl maps to mouse chromosome 8 and has been annotated on supercontig NW_000344.1. The Component map shows the tiling path of the GenBank records used to create the Contig map. Supporting EST evidence and a link to the corresponding UniGene cluster are displayed on the UniGene map, while observed polymorphisms within Lpl are shown on the Variation map. The Genes_ seq map provides links to other NCBI resources and molecular data, including LocusLink (Lpl link), Sequence Viewer (sv), Evidence Viewer (ev), Lpl gene sequence (seq link), Human-Mouse Homology Map (hm) and a link to NCBI’s Model Maker (mm). When a ruler is displayed alongside the Genes_ seq map, nucleotide sequences flanking Lpl can be obtained by following the seq link or Download/ View Sequence/Evidence link and specifying the region of interest. Additional information adjacent to the Genes_seq map includes an arrow that shows the direction of transcription and an evidence code that indicates the type of evidence used to construct the gene model. Try the Mouse Map Viewer from the Mouse Genomic Biology Page.

Data from the two genome assemblies can be downloaded via FTP at For additional information, click on the ‘help’ link in the Map Viewer. 


NCBI News | Spring 2002 NCBI News