WebChrom HELP

WebChrom is a web based graphical display to browse the chromosome for markers and contigs of FPC database.

Chromosomes (or Linkage Groups) Display

 WebChrom graphics is generated from a FPC database. FPC allows contigs to be assigned to a position on a chromosome; such contigs are referred to as 'anchored' contigs. The Chromosome display shows the positions of each anchored contig.

If there are sequenced clones that have been entered into FPC as simulated digest clones, the location of each clone is shown as a green line.

Click on a chromosome to view the expanded view.

Expanded view of a chromosome

The contigs and frameworks are shown ordered along the chromosome. FPC can contain a set of ordered markers, which are generally from a genetic or radiation hybrid map. These ordered markers are referred to as anchors. The well-ordered anchored are referred to as frameworks and the binned anchors are referred to as placements. Only the frameworks on shown on this display.

The length of the contig corresponds to the the position of its corresponding frameworks. If two contigs overlap based on their frameworks, the algorithm computes the framework which is most likely to be wrong, and a yellow unbounded box is drawn to that framework. Hence, no 'bounded' yellow boxes overlap.

Following section describes the details that can be view in WebChrom for contigs and frameworks.

Information for contig
Put the mouse over a contig and click, a popup will display the following informations:
View in WebFPC click this and it will display the corresponding contig.
x - y cM the first and last framework.
n total clones the number of clones in the contig
n sequenced clones the number of sequenced clones.
n unique markers number of markers in the contig.
Max CB value: n the length of the contig is in CB (consensus band) units, where one CB is approximately one restriction fragment. With agarose gels, a fragment is approximately 4096 bp, so multiply n x 4096 gives the approx length of the contig in bp.
CB x - y covered by FWs: x is the position of the first framework and y is the position of the last.
n framework(s) hit in the chr total number of framework.
Also hit .... this lists if any of the frameworks hit other chromosomes.

Information for framework
Put the mouse over a marker and click, a popup will display the following informations:
View in WebFPC click this and it will display the corresponding marker in WebFPC. If the marker hits multiple contigs, a list of the contigs will appear, else the contig for the marker will be displayed.
... There may be links to other databases with information about the framework.
Position x the cM position.
Hit n the number of clones it hits on each contig that contains it.