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

Click any image to view an enlarged image.

Demo-Seq to Demo-Seq2

	Click an image to view a closeup.
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.
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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.
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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.
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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

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

There are a few off-diagonal blocks, which may indicate repetitiveness (but these blocks are probably too small to be meaningful). Click to view summary

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
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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. Using the Blocks view, note that they major blocks are the same, as they should be.

The first two lines of each is:

>>> SyMAP v5.6.1 (27-Jan-25) Running Java v17.0.11 on 27-Jan-25 11:47:49 <<<
>>> demo_seq to demo_seq2 Verbose (or !Verbose)

The last 6 lines are the Summary (not shown). As is obvious, most of the "verbose" is during the cluster algorithm.

Algo1, !verbose

Cluster Algo1 (modified original)
Warning: 2 alignment files exist - using existing files
   If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
Scan files to create candidate genes from hits
    20,005 Total scanned hits
Scan files to cluster and filter hits
    11,000 Total cluster hits
     6,816 Filtered hits to save
Finish load hits                                   154.10Mb         7s

Finding synteny for demo_seq and demo_seq2
        18 Blocks
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny                       5s

Finding Collinear sets
       717 Collinear sets
Finish Collinear                     0s

Algo1, verbose

Cluster Algo1 (modified original)
Warning: 2 alignment files exist - using existing files ...
   If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
Loading annotations
    10,108 demo_seq genes
    10,137 demo_seq2 genes
Scan files to create candidate genes from hits
    14,058 scanned PROMER demo_seq_cc.demo_seq2_f1.mum
     5,947 scanned PROMER demo_seq_cc.demo_seq2_f2.mum
    20,005 Total scanned hits
Scan files to cluster and filter hits
     6,923 clustered demo_seq_cc.demo_seq2_f1.mum
     4,077 clustered demo_seq_cc.demo_seq2_f2.mum
    11,000 Total cluster hits
Filter hits
     8,556 for demo_seq
     7,350 for demo_seq2
     6,816 Filtered hits to save
Save results
   Save filtered hits
   Save hit to gene
     6,564  (6,375) for demo_seq
     6,564  (12,749) for demo_seq2
   Compute and save hit#
   Compute and save gene numHits
Finish load hits                                   117.44Mb         6s

Finding synteny for demo_seq and demo_seq2
     6,816 Total hits
         4 group-x-group pairs to analyze
        18 Blocks
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny                       5s

Finding Collinear sets
       717 Collinear sets
     1,969 Updates
Finish Collinear                     0s

Algo2, !verbose

Cluster Algo2 (exon-intron)
 G0 length scale = 0.5
Warning: 2 alignment files exist - using existing files
   If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
   Final totals
        4,759 Clusters  Both genes    4,713   One gene       34   No gene       12
        6,883 Filtered  Both genes    3,263   One gene    2,453   No gene    1,167   Pile hits 7
Finish load hits                                   95.47Mb          6s

Finding synteny for demo_seq and demo_seq2
        18 Blocks
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny                       2s

Finding Collinear sets
       635 Collinear sets
Finish Collinear                     0s

Algo2, verbose

Cluster Algo2 (exon-intron)
 G0 length scale = 0.5
Warning: 2 alignment files exist - using existing files
   If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
   Load genes for Algo2
      Demo_Seq2  [Avg Min Max] [Gene 2,968  120   89k] [Intron   430    1   87k] [Exon   294    3 4,935] Cov 46.5%
      Demo_Seq   [Avg Min Max] [Gene 2,575   63  508k] [Intron   373    1  501k] [Exon   379    1 6,153] Cov 57.8%
   Load demo_seq_cc.demo_seq2_f1.mum  Hits 14,058 (EQ 2,893 NE 11,165)
          3,038 chr3-chr1 Clusters    Both genes  3,022   One gene     13   No gene      3
            490 chr5-chr1 Clusters    Both genes    484   One gene      5   No gene      1
   Load demo_seq_cc.demo_seq2_f2.mum  Hits 5,947 (EQ 2,366 NE 3,581)
            429 chr3-chr3 Clusters    Both genes    417   One gene      7   No gene      5
            802 chr5-chr3 Clusters    Both genes    790   One gene      9   No gene      3
   Final totals
        4,759 Clusters  Both genes    4,713   One gene       34   No gene       12
        6,883 Filtered  Both genes    3,263   One gene    2,453   No gene    1,167   Pile hits 7
   Compute and save hit#
   Compute and save gene numHits
Finish load hits                                   96.43Mb          6s

Finding synteny for demo_seq and demo_seq2
     4,759 Total hits
         4 group-x-group pairs to analyze
        18 Blocks
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
   Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny                       2s

Finding Collinear sets
       635 Collinear sets
     1,714 Updates
Finish Collinear                     0s

>> Summary for demo_seq to demo_seq2
     4,759 hits
        18 synteny blocks
     4,747 gene hits
     3,260 synteny hits
Complete Alignment&Synteny           10s