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SyMAP Tour |
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Contents
| Management: | High-level views: | Detailed views: | Analysis: |
Project Manager
After the synteny database has been build (see System Guide), the synteny can be viewed from the manager. All projects in the database will be listed on the left panel.
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Selecting projects on the left panel shows them on the right panel. A check mark in the
By selecting a cell with synteny,
the The | 
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Chromosome Explorer | Go to top |
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Multiple chromosomes can be selected
from different species on the left-hand panel.
The default display is the Circle view shown. From here, one can select Dot Plot or 2D. For Circle and Dot Plot, multiple chromosomes can be selected and viewed (as shown below). For 2D, it is best to only have two or three chromosomes selected (as shown below). | 
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Circle View | Go to top |
The left image shows all chromosomes for cabbage and B.rapa. The right image shows Cabbage chr1, B.rapa chr2, and A.thal chr3 and chr4.
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Dot Plot | Go to top |
The left image shows all chromosomes for cabbage, R.rapa and A.thal. The right image shows Cabbage chr1, B.rapa chr2, and A.thal chr3 and chr4. Synteny blocks are outlined in blue, and one can click to zoom further and arrive at a more detailed 2D display.
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Block View | Go to top |
The synteny blocks are colored by chromosome (see color key at top).
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Clicking a chromosome pops up a window of the chromosome as shown below. Clicking
a block pops up a 2D display.
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2D 3-Chr
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This is a three-chromosome view.
The dark blue and purple down the center of the chromosomes are annotated exons, where blue is positive strand and purple is negative strand. The brown and green lines between chromosomes are hit-wires connected the similar region on the two chromosomes. The brown are hit-wires with the same orientation on both connecting chromosomes and the green are different orientation. Only hits that are part of a synteny block are shown here. | 
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2D 2-Chr | Go to top |
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This is a two-chromosome view.
The A.thal Chr4 and Cabbage Chr1 were displayed, a region was selected and the right track flipped. The genes are staggered if they overlap by more than 3 bases. The thin rectangles near the edge of each track are the hit regions connected by the hit-wire. | 
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2D Closeup | Go to top |
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The image on the right shows a smaller region with the A gene can be right clicked to view a popup of extended information, including the exons and hits. The hit-wire can be right clicked to view of popup of details of its information. | 
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Base View | Go to top |
| It is possible to zoom in even further and see a basepair-alignment of the hits in the region. | 
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Query Interface | Go to top |
Query Results | Go to top |
The PgeneF number is a unique number assigned to the gene family.
The PgFSize number is how many unique instances are in the family.
Multiple alignment | Go to top |
