Introduction

VCMap consists of two main resources - VCMaps themselves and the VCMap build data that underlies the maps. This help section is divided into two sections, the first describing the VCMaps, the second describing the various reports that can be accessed from the VCMaps and by querying the VCMap build data. A manuscript describing the map construction and algorithms used is in final revisions for publication, (Kwitek-Black etal. 2001). For further information please use the RGD contact form.

• Help for the VCMaps
• Help for the VCMap reports
  • Individual Marker Report
  • Chromosomal Region Report
  • Map Data Report
  • VCMap Predictions (Virtual mapping)
  • Bin Prediction Report
  • Stream Prediction Report

The VCMaps

Below is shown the top section of the VCMap for Rat Chr 1 [ Open this VCMap ]. Rat is the backbone organism and Chr 1 is shown in color in the middle of the diagram with syntenic regions of Human and Mouse shown to the left and right respectively. As this is a static image there is a limit to the number of markers that can be shown whilst keeping the image to a reasonable size, consequently only a proportion of mapped markers can be shown. The locations of other markers on the backbone strain are indicated by black tick marks and clicking on the shaded intervals of the backbone strain will bring up a Chromosomal Region Report for that interval listing all markers in the region.

Mapped Genes, UniGenes and STSs are shown on all chromosomal segments, anchor lines are shown connecting markers in different organisms predicted to be homologs by the VCMap alogorithm only where both markers are visible on the graphic map. Markers shown in red on the backbone map are RH framework markers, all other mapped markers are shown in black. Clicking on the framework markers will take you to a map data report for that marker, clicking on a Gene/UniGene will take you to the individual marker report.

The chromosome number of the syntenic regions is shown in blue above each syntenic chromosomal segment. Clicking on this chromosomal number will bring up the appropriate organism's VCMap for that chromosome, eg. clicking on Chr.06 above the Human chromosome 6 segment will bring up the VCMap for Human Chr 6 (Human will be the backbone organism, Rat and Mouse syntenic regions will then be shown for HSA6). Please note that you may have to search a little to find the corresponding region on the new map, in the example shown the corresponding segment of Rat Chr1 is right at the bottom of Human Chr 6. [ Open this VCMap ]

VCMap Reports

Individual Marker (Gene, UniGene, and EST) report

Example: Query result for Rn.14443 [ View this VCMap Report ]

This report displays the underlying VCMap build data for a particular marker including the ESTs and UniGenes that were involved in creating the relationship and the best blast result scores between sequences from the Backbone and Reference UniGene clusters.

Chomosomal Region Report

Example: Genes and UniGenes (markers) between 0.0 cR (Centi-Ray) and 51.4 cR in Rat Chr.01. [ View this VCMap Report]

The chromosomal region report is a combination of UniGene data and RH map. Results from RH map carry the placement lod score (eg. P>3.0 indicates a placement at greater than LOD 3.0). Framework markers are denoted as letter ‘F’s. Whenever available, the UniGenes will also follow by gene symbols. Clicking on any of the UniGene IDs will take you to the individual marker's report, shown below.

Map Data Report

Clicking on any of the SSLP markers from the VCMaps or on any of the reports will display a Map Data report such as this one shown for D10Got105 listing the locus name, position in centirays, LOD score of placement (or F for framework marker) and a list of aliases - alternative names for this marker in RGD and other databases. Genetic map data is also shown for Human markers.

Map data for Rat, Mouse and Human was obtained from the following sources:

• Rat: Rat Genome Database, http://rgd.mcw.edu
• Mouse: Whitehead Institute: http://www-genome.wi.mit.edu/mouse_rh/
• Human: GB4 RH maps (NCBI GeneMap99, raw data: EBI http://corba.ebi.ac.uk/RHdb/species/HUMAN/gm99.html)

VCMap Predictions

When the gene or EST of interest is not mapped, a prediction can be made if the position of the homologous gene or EST in the reference (non-backbone) species is known. The gene (UniGene) prediction is based upon the BLAST result and the known syntenic region of chromosome between the different species. The borders of chromosomal conservation are also known as the chromosomal breakpoints. They are referred to as anchors in VC Map.

Two kinds of predictions are available for VC Map, Bin and Stream predictions.

• 'Bin' - Prediction within two anchored markers (defining the limits of the bin)
• 'Stream' - Prediction outside a bin, only one anchor.(prediction is up or down stream of the anchor)

Bin Predictions

A 'bin' prediction is made by predicting the location of the homologous UniGenes of the backbone species, based upon the mapped borders (breakpoints) of the homologous region of the reference (non-backbone) species. The position of the predicted UniGene is defined by the first flanking UniGene anchor (Anchor1 UniGene) and its position (Anchor1 Position), and the second flanking UniGene anchor (Anchor2 UniGene) and its position (Anchor2 Position). This is shown diagramatically in the example below:

The top of a bin report for the Rat Chr01, 0-54cR region is shown below: [ View this VCMap Report]. An explanation of each column heading is provided in the table below.

Stream Predictions