SyMAP Demo

SyMAP Demo Results

Contents:

Demo-Seq to Demo-Seq2
Self-synteny of Demo-Seq
Demo-draft to Demo-Seq2

The demo was created from real data >15 years ago, and is VERY obsolete - it is strictly for demonstration.

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Demo-Seq to Demo-Seq2

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This document shows the different views for the `Demo-Seq` to `Demo-Seq2` alignment. When synteny has been computed for the demo, the table will have a checkbox, signifying that the synteny is available for viewing. The cell will be highlighted green, which will enable the viewing buttons, e.g Dot Plot.

Click Dot Plot and you will see the dot plot shown here. By clicking and/or selecting regions you can zoom into certain regions and bring up detailed views of the alignments. The Help button (question mark) provides full information on the functions.

Return to the Manager, and click the Chromosome Explorer button. This brings up the Explorer. The top left chromosome icon will have its number highlighed in a red box; this indicates it is the default reference chromosome. Click on the icon body for `Demo-Seq2` 1 and 3 (i.e. chr1 and chr3) to see the Circos-style³ view shown on the right. The ribbons represent synteny blocks.

Click the 2D button to see a side-by-side view of the same chromosomes. Note that the reference is in the middle. The lines between chromosomes indicate the individual clustered hits.

A region of one of the chromosomes was selected to zoom in, as shown in the image on the right. The exons for individual genes can be seen in the center of each sequence track. The length of the hit is shown on the inner boundary of the each chromosome segment. There is a sequence filter for Annotations. This will show the annotation as shown on the right, but it must be zoomed in close enough. Alternatively, as long as the view is zoomed enough to see the individual exons, right-click on a gene for a popup of the annotation.

Returning to the Manager, click the Queries button. This brings up the query window in Overview mode. Click the Query Setup option on the left-hand side and you will see the corresponding window:
Using the query setting from above results in this table, where columns can be changed, sorted and moved.

Algo1 versus Algo2

The following show the summary when the Synteny Clustering was run with Algo1 versus Algo2.

Self-synteny of Demo-Seq

Demo-Seq has been run against itself, resulting in the Dot Plot shown on the right. There are a few off-diagonal blocks, which may indicate repetitive-ness (but these blocks are probably too small to be meaningful).

Click to view summary

Demo-Draft to Demo-Seq2

The `Demo-draft` was run against the `Demo-Seq2` with its order_against parameter set to `Demo_Seq2`. The resulting dot plot is shown on the right. Note that the 43 contigs are ordered, but still fragmented. Click to view summary

When the ordering algorithm is run, it creates a new project called `Demo-Draft_ordered`, where the 43 contigs are written into three chromosomes; the first two correspond to chr1 and chr3 of `Demo_Seq2`, and chr0 contains the contigs that do not align.
The new project `Demo-Draft_ordered` was aligned with `Demo_Seq2`, resulting in the dot plot shown on the right. Click to view summary

The `Demo_Draft` was created from the `Demo_Seq` with sequence reversal and some other changes. In the snapshot on the right, the blocks of the `Demo_Seq`-to-`Demo_Seq2` are shown next to the blocks of `Demo_Draft_ordered`-to-`Demo_Seq2` is shown on the right. Note that they major blocks are the same, as they should be.

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