Getting Started Using MapViewer

Genomic analysis: it's all about location

We can better understand how an organism's genome functions if we know the location of important features; genomic analysis involves the "reading" of the nucleotide sequence and the localization of important features along the chromosomes. The more information we have about feature location, the easier it is to determine the significance of any particular region.

Scientists are gathering information about the features found on the genomes of various organisms at an incredible pace; they are identifying genes, gene-regulating regions, phenotypic markers, and sites of variation, to name just a few. However, the exact chromosomal location of many of these features has been elusive. By integrating feature identity information with whole genome sequencing results, we can get a more complete and accurate view of the genome. NCBI's MapViewer is an alignment viewer designed to perform this task for you.

You can get to MapViewer through various routes.

What is MapViewer and what can it do for you?

What is MapViewer?

The NCBI MapViewer is an alignment viewer for data from both genetic and physical maps (where a map is a collection of a specific type of data). Genetic maps provide information on the order and proximity of genes in relation to each other as a function of co-inheritance frequencies; that is, the closer two genes are to each other the more likely they will be inherited together. Physical maps provide information on the physical location and sequences of features. Currently, these maps are "works-in-progress" and incomplete; however, we can construct a more complete genome map by cross-referencing the available data resources using shared markers. MapViewer uses this system to integrate the various types of genomic mapping data, thus strengthening the accuracy of genome analysis. In addition, because MapViewer presents these data sets as "connected" maps, you can see the connections among the different types of data.

You can search the genomes of many different organisms using the NCBI MapViewer. Mouse-over the organism name below to get a description of the data sources utilized by MapViewer for that organism and to link to its MapViewer page.

What can MapViewer do for you?

Because each MapViewer displays a collection of available data for a particular genome, you can use it to find the sequence and/or location of genomic features like the genes on a particular chromosome, the markers proximal to a gene of interest, the known or predicted gene transcripts and splice variants, or regions of a chromosome associated with a particular disease. And because MapViewer displays alignments between the various types of map data, you can use it as a cross-referencing tool. For example, you can use MapViewer to determine the genomic location of your sequence and whether it is an expressed or regulatory region. You can also use MapViewer to determine which BAC contains your gene of interest. The MapViewer is a versatile and multifaceted tool.

With just a few basic skills, you can get the genome information you want using MapViewer. To get started using MapViewer, check out:

Additional information about MapViewer is available by clicking on the following:

• MapViewer Help Document
• NCBI Handbook-Chapter 20: Using the MapViewer to Explore Genomes
• MapViewer Exercises