• What is VCMap?
• What maps are used in the calculations?
• How do I find comparative mapping information about a gene or marker?
• What information do you have on each marker?
• What other information can I get to via VCMap?
• Detailed VCMap Help
• Let me use VCMap...

Virtual Comparative Map (VCMap) is a computational tool that facilitates in silico prediction of syntenic regions between rat, mouse and human. It utilizes the available map information for markers and ESTs (Unigene) from all three species. The output of this comparison is a comparative map providing a visual representation of the chromosome of the primary (backbone) species plus syntenic regions from the two other species. The maps are clickable allowing you to view further information on the mapped markers and clusters plus bin reports showing the build data for a defined chromosomal region.

Mapping data used in the current VCMap build (v5, July 2002)

• Rat: RH map v2.1, Rat Genome Database, http://rgd.mcw.edu
• Mouse: Mouse RH map Release 9, Whitehead Institute; http://www-genome.wi.mit.edu/mouse_rh/
• Human: GB4 RH maps (GeneMap99, http://www.ncbi.nlm.nih.gov/genemap99/)

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There are two ways to search the VCMap data:

1. By querying the VCMap data for a particular marker (query by gene, unigene or accession number)
2. By displaying a particular region of the maps (query by species/location)

To obtain more information, click on Search VCMap from the Detailed Help and follow the instructions.

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All the microsatellite markers on a VCMap prediction output are hyperlinked to their reports in RGD. All the Unigenes and known genes from different reports are hyperlinked to NCBI Unigene or GenBank respectively.

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Apart from producing visual representation of the syntenic regions from the three species, VCMap also generates individual reports for markers, chromosomal regions, map data bin predictions and stream predictions. Descriptions of these reports can be obtained from the following detailed VCMap help pages [ More... ].

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The detailed VCMap Help pages provide you more details about how to use VCMap quickly. Please follow the steps:

1. Introduction
2. Starter's Guide
3. View VCMap
   • 3.1. Display a static map
   • 3.2. Display Dynamic maps using MapView
4. Search VCMap
   • 4.1. Search Marker
   • 4.2. Query by Chromosome Region
5. Query Reports
6. VCMap Glossary

   The whole VCMap Help document - Printable Version.

Go to view the detailed VCMap Help pages now.

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